I have checked till I am blue in the face. Prefer economy + seats; this is to coincide with a river cruise starting in Praque, with a couple of pre cruise dates, and returning to US.

If you are having trouble finding good/affordable flights and are flying in a few days early, why not look at flights into any major hub of your favorite airline(s). Then you can book a separate ticket on any airline, low cost or otherwise, or even a train, from your arrival city to Prague.

What specific help are you looking for?
Price, availability, alternate ideas?

The list price for Econ + tickets for 6mo from now to various places in Europe that I've looked at seem to be in the $3000 per seat range, round trip. One option to roll the dice on is buy a coach ticket, then look to upgrade at a later date. I've done this before, and the airline continued to lower the price for Econ + seat upgrade as travel date neared. The ability to do that will likely depend on the airline and the route.... So it's a gamble...

Hard to be of help without knowing what the problem is.

I guess you don't want to say what your problem is in terms of checking but not finding whatever. It depends where you are flying from. I fly from IAD East Coast, so for me, I prefer Delta/AF or United for European flights as I can fly to various hub cities nonstop from here.
Delta/KLM/AF would have Paris or AMS as the flight, then a transfer to/from PRG or Budapest. United would have FRA or maybe MUC. Those would work for me.

I hate BA so won't fly them if I can help it, but they would have London as a destination for those cities. IBeria is their partner and has such flights also, but their hub is Madrid and they also go to them.

We need a lot more info in order to help. If you're looking for a good deal for Premium Economy, I have an upcoming trip on Finnair and I popped for Premium economy because it is a better deal on Finnair than most. I checked and they do fly to Prague and Budapest. Of course, a lot depends on your home city.