I tried to edit my original post to have this on there, but didn't see a place. Should I just reply all with it? Sorry, I am new to Fodors, so I'm not familiar with their formatting/rules.

Thank you very much for the info on the train! We looked on multiple places and saw $75-80. Is there a website that shows them all or a trick to knowing we should have looked on that specific one?

You don’t have to edit your first post. Just add new ones to update people on your current thinking.
If you are going to Vienna, why are you flying from Basel to Budapest? Vienna should probably be your last stop before Budapest. How are you proposing to get to Basel?
You say you are on a budget, but not what kind. I can tell you that Basel is expensive! I certainly would not spend two days there anyway. Actually, I would somehow plan to skip it. It is an OK stop, but sure not up to the level of interest of other places, IMHO. I would also not spend four days in Colmar with only a day trip to Strasbourg.

Now, honestly, I am sorry, you are still all over the place. You are going to the eastern most end of Austria. You are going to a bit of Germany. Somehow you are then going way west, to the most south western tip of Germany, going up to Strasbourg and back to Basel to fly to Budapest, east of Vienna. This is just as convoluted as your first itinerary.
You still need that great big paper map, preferably one with train lines!

Cheap flights do not necessarily mean cheap travel. It can just muddle things up when it takes you out of your way or to places in which you have no interest.

Do you love museums and great Art of the Renaissance? If so, Florence is your cup of tea. Any interest in Siena, Pisa, etc?
Do you enjoy cold and wet and windy? You might get lucky, because that is likely to be the weather in Venice.

I can see you are really, really trying, but not making good progress. You want to see things. It looks as if certain places are pretty important to you. Block those in and see how they can be connected.

You have proposed days in places that do not work because you have not accounted for travel time. It will take 1/2 day from Florence to Venice, not just train time, but getting to the train station in Florence, getting to the hotel in Venice, etc. takes time. It will take a day from Venice to Vienna, a day from Basel to Budapest, etc. depending on flights.
You also want to go cheap. Flights can work, but often trains are better and save time if you have a well planned itinerary. Trains go mostly city center to city center, so no treks to airports with lines and waiting.

One issue is that you must get to Budapest at a planned date. Work towards that. Please get that map.

Thank you very much for all the suggestions! We have created the below itinerary based on some of the feedback.

We're looking for any recommendations that you may have from your experiences! Are there any of the locations in which you think we need more or less time? Do you have recommendations for the towns as far as what to eat, sights we must see or activities we must do?

Florence 3 days

Venice 4 days

Vienna 3 days

Salzburg 2 days

Nuremburg 4 days

Rothenburg 1 day

Colmar (w/ day trip to Strasbourg) 4 days

Basel 2 days (Should we add a day trip to Lucerne?)

A few notes-
We chose these towns because they seemed interesting based on your suggestions and our research, but are certainly open to modifying it. We chose Basel because it was close to Colmar and has direct flights to Budapest. We know going to Budapest afterwards does not make sense logistically, but it is already planned and booked because that is the section we are doing with family. We also looked at doing the route in reverse, but either way we would need a flight to Budapest and this way was cheaper, while still being direct.

Thank you for all the replies! We are trying to get a lot in because we don't know when the next time we will get to do a month+ long trip in Europe. We are expecting to spend at least $9k on this first part of the trip before we hit Budapest. We care more about seeing the cities, sights, and trying the unique foods more than hotels, so we will be staying in budget friendly hotels/hostels. We do have the travel times all planned in on our detailed itinerary, so we are okay with those half days being used. When we are in a city, we like to wake up early and not get back to the hotel until very late. We don't go to bars/clubs, but just love walking around and experiencing as much as we can in the short time that we have. We have used the trains/travel time as our downtime and naps to recharge before the next city.

We really care about Venice, Nuremburg, Rothenburg, and Colmar. The other cities were added due to recommendations or logistically (Direct flight from Basel to Budapest).

You can use www.bahn.com to look for timetables and pricings for the whole of Europe. It's the German railways website but delivers more than just Germany. You should confirm pricings and information on the national rail websites. For Switzerland www.sbb.ch, for France www.sncf.com, for Italy www.trenitalia.com, and for Austria www.oebb.at . They all have English-language options (you usually find this in the top right-hand corner). You can buy your tickets from all of those sites. I personally prefer not to use a third-party site, it won't be the cheapest option. Prices are usually cheaper the sooner ahead you book your trip (3 months).

A useful website for train travel is https://www.seat61.com . He sometimes posts here, but basically he has taken his hobby of train nerd and turned it into a profitable and useful tool for people learning about train travel in Europe. You will glean a lot of information from him.

Lavandula

Lavandula and Op. The site is seat61.com , the "the man at" link just takes you to search/dead end page.

We have merged a 3rd thread into the original topic.

Lavandula and Bilboburgler, thank you very much! This train information is very helpful!

For someone who has "previously traveled to Amsterdam, Prague, and Rome" there is a singular lack of understanding about European travel. Go to the library and peruse through the city guidebooks that you can find, or regional ones, so that you can figure out what you want to see specifically and then how to organize your train travel from one destination to the other.

We have already looked at the travel between the cities and did plan it out, so I'm not sure what exactly you are referring to.

Fly into Florence, high speed train to Venice, direct flight to Vienna, high speed train to Salzburg, train to Nuremburg, train to Rothenburg, bus/train to Colmar, train Basel, then a direct flight to Budapest. Most of our trains are an hour or 2 and our longest is Rothenburg to Colmar. We really want to see Rothenburg, so we are okay with the longer travel to get there/travel from there.

What specifically are we missing?

Now that you have the itinerary planned out, and you do not mind the times, it looks good and gives you all the cities that are important.

Look at possibly a couple of small changes.
Reverse the trip from Venice onward, flying from Venice into Basel rather than into Vienna.
End in Vienna, take the train to Budapest and save the hassle of two flights.

After Colmar, since you could go in that direction anyway, stop for a night in Strasbourg on the way to Rothenberg. I guarantee, based on your enjoyment of walking around soaking up the ambiance of places, that you will find a night there worthwhile.

That is a great change that we had not thought of. Thank you very much!

We will take 1 night from Colmar so we can spend a night in Strasbourg, so the new order will be:

Florence 3 nights
Venice 4 nights
Basel/Lucerne 2 nights
Colmar 3 nights
Strasbourg 1 night
Rothenburg 2 nights (with the travel time to get to Rothenburg from Strasbourg VS Nuremburg we added an extra night here to make up for it)
Nuremburg 4 nights
Salzburg 2 nights
Vienna 3 nights
Budapest 6 nights (family planned, so pace slows down)

Regarding your latest itinerary - I suggest less time in Nuremburg, more time in Salzburg and (if possible) more time in Lucerne.

Oh, thank you for correcting, bilbo, much obliged.

Lavandula

We edited your post #26 to correct the URL

Hope you are still reading because you asked earlier for tips on food, etc. A few to start. Sorry if things are misspelled. Being lazy tonight.
Germany
Nuremberger (Nurnberg sausage) Wurst.
Be sure to have this. It will be at markets and casual places and bratwurst stands. It is not like any other Bratwurst. These are small, about finger sized. Have them grilled (rosted) three on a bun. They may be boiled a bit first, but you want grilled. Kraut and potato salad is extra cost, but worth it if you like it. Otherwise, mustard. This may sound crazy, but there is actually an EU protection in place requiring these to be made in Nuremberg to a specific, size, recipe, etc. I am not a fan of the big, fat Bratwursts you see everywhere, but the Nuremberger wurst is a real treat. They are also, not cheap.

Schokokuss. (Chocolate kiss) may be called foam kiss or other things. Not taking time to look up. It may be spelled differently. Anyway, this is the most melt-in-your mouth confection. It is the lightest marshmallow cream you can imagine, like air (nothing like our thick, sticky, sugary, marshmallows), contained in a thin shell of German Chocolate set on top of a thin wafer. You will certainly see them in the outdoor markets. They do ship to the states, but they are often a melted, stale, broken up mess. Get them fresh while you can. Look up pictures. They are about 1&1/2 inches tall, dome shaped and 1” wide.

Leibkuchen, (forget spelling) firm to hard, gingerbread-like spicy cookie. They may be different shapes, but hearts are common and were given to a sweetheart, friend or family. They will see them everywhere. You will see them on ribbons or strings hanging around little kid’s necks. You can have something written on it. Buy a heart for your GF and share while you walk around.
At Casual places in Germany, you may be seated at big round or long tables with other people. Do not be put off by it. It is common and fun to meet people.

Italy is different. Especially in Northern areas like Venice, it is considered courteous to reserve a table, even in very casual restaurants in the evening. You will be greeted warmly and a table will be waiting. It does not have to be far ahead. If we know ahead, we reserve ahead, but we have even seen a place we liked and popped in and reserved for an hour later and just walked around to fill the time and return. Guests do not arrive at your home unannounced. So, in Italy, don’t be a tourist just walking in and expecting to be seated. Be a welcomed guest.

How on earth has this chocoholic who visits Germany at Christmas as often as possible missed out on Schokokuss?

Thanks for the tip Sassafrass.

Schokokuss and slight variations are made through out Europe. Some countries originally had names that are unacceptable now.

Probably because it is not a chocolate. The thin chocolate skin just holds it together.
I kept thinking of the filling as marshmallow cream, but know it is very fragile, so looked up recipes. It is more of a meringue made with fresh egg whites (hopefully pasteurized) and gelatin syrup to make it creamy. Fresh ones are best within two or three days. We always thought of them as treats for the children, but as you can tell, adults like them too. It is one of those simple things that you have as a child and remains in your memory ever after.