Rent a car and do it all independently. We spent time in Seward, on the Kenai River at a fishing camp where we caught King Salmon and trout, Homer, Alyeska at Girdwood, Anchorage and Talkeetna. We liiked Homer a lot, took a ferry across the bay, took a float plane on a day trip from Homer to the next peninsula to the west to Katmai NP to see the bears catching salmon and ambling about. Girdwood was a nice stop too.
We flew from Anchorage to board our small expedition ship in Juneau. Driving was easy in Alaska and I don't see why a tour would be needed at all. It was easier than driving in major US National Parks in the west.

I did the cruise tour with Celebrity and given the chance again would do the tour on my own. In Denali we did the tundra wilderness tour with the outfitter that was provided by the cruise and licensed to go into the park. The only way you can go into the park is on a bus, but the park service has busses that are less expensive and go on the same (only) road in. You can to much farther on one of them. We did see lots of animals and were there in early September so the tundra was a beautiful pink/purple with areas of yellow absolutely breath taking. You would see the same things going with the park service and be able to get off and hike if you wish and then get on another bus.

I can't really compare costs, but would guess that you could do it all on your own for the same or less money, since the cruise line makes money on these trips.

By all means, do it yourself. You will gain flexibility and save $$$.

"Is the Kenai Fjords National Park Cruise worth doing?"
Yes, very much so.

"Another post has recommended Homer, which we would have to do independently. Should that be a priority?"

Time permitting, sure. But not just for the destination (Homer), do it for the drive too. You'll go through a small town called Ninilchik where you can stop to see a very picturesque Russian orthodox church. This is a good place to stretch your legs and get a great photo op.

"If we were going to travel independently, should we rent a car or can we get where we need to go by rail?"

You can't go everywhere by rail (e.g. Homer). My preference is for the car because you can stop where and when you want. In Girdwood, about 30-40 minutes south of Anchorage, there are several things of interest (Wildlife Conservation Center, Mt. Alyeska tram) that are impossible to see if traveling by train.

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Vic's travels: http://my.flightmemory.com/vogilvie

Since you have done Europe independently and dislike bus tours - rent a car and do it on your own. Either way, Kenai Peninsula and Denali are in opposite direction from Anchorage so you need about a week.

It is really quite easy as there are not a lot of roads to choose from in Alaska. My preference is car since it gives you greater flexibility - and the road and train tracks are parallel and very close on much of the route, so scenery is not all that different.

The Kenai Fjords water tour is well worth it - think of the cruise as giving you a maxi-view and this giving you a micro view of glaciers, animals. Take the longer all-day one. We spent a couple of days in Seward, a few days at Denali and the rest on transiting from one to the other or in Anchorage between. It was suggested that we not try to drive all around Kenai Peninsula in the time we had and we opted for just one town rather than a drive-by of more. It seemed like the right decision.

As you plan, be prepared for sticker shock - especially for rental car. It almost made me want to cancel our trip! But with 4 people to share cost, my guess it would be less than the train. Figure meals are going to cost you what they would in a large expensive city - even in the middle of nowhere. Everything else is about 20% more than in the real world.

Thanks everyone for your advice; it's very helpful. Any thoughts about the value of staying in one of the lodges at the end of the road in Denali vs. a lodge or B&B at the entrance? Is it true that it is a several hour bus ride all the way in to the Park?

There are good accommodations in nearby Healy. Several years ago, we stayed at the Denali Dome Home and were very satisfied. http://www.denalidomehome.com

"Is it true that it is a several hour bus ride all the way in to the Park?"

Yes, depending on which shuttle bus tour you take.

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Vic's travels: http://my.flightmemory.com/vogilvie

We took a 13 hour bus tour into Denali - all the way into the end, with a 3 hour stop at the lodge there for lunch, light hiking, activities. It was exhausting and although I am glad we did it since I doubt I will ever be back that way again, it had some negatives. First - a school bus for all those hours with short stops along the way gets old very fast. We were fortunate enough to see a lot of baby animals in early spring, some very close up. But there were hours of just riding. Also, the un-guard-railed switchbacks and cliffs were a terrifying experience for my son and me since we are height-phobic. The gravel road is about the width of 1 1/2 busses - and when you meet an oncoming vehicle they almost touch each other trying to inch by - the outside one with wheels inches from instant death.

We did the scheduled bus trip rather than shuttles with independent stops since I wanted the security of actually getting into and out of the Park and not flagging down a shuttle.

We were told there are some decent day hikes from near the entrance to Denali from the Park Office. (Aren't you worried about bears?)

You have a choice of trips into Denali. The shortest would be to take the park service bus and get off when you get antsy and hope for a return bus to pick you up soon for the trip back. The concessionaire tours generally are 4, 8, or 11 hours. We took the 8 hour tour which was the longest that our package allowed. They provided a box lunch, water and hot drinks. The naturalist on the bus also had a zoom camera that was connected to drop down screens so he could focus on a distant animal, like a grizzly and project it onto the screen so that people who didn't bring binoculars could have a close up view. We did have a moose couple walk right in front of the bus, the bull was in hot pursuit of the cow, also lots of dall sheep very close to the road, as well as bears, etc. If we go again, I would take the longest trip possible as the farther in we got the more animals we saw. Do get lunch, snacks, drinks for your trip.

Thanks everyone. I think that we will do the land portion independently. I am looking at Skyline Lodge for two nights with the fly in/bus out option. Really looking forward to it!