First of all, welcome to the forum. The 3rd gen section here doesn't get much traffic, especially for the carbie ludes.
You don't have a 2 barrel carb, you actually have two side draft carbs (basically motorcycle carbs). There are a lot of things that can go wrong with these, and it's not advised for you to do anything with them until you do a LOT of research on them.
You can try a couple of simple things first. Buy a bottle of HEET fuel line drier. Some of your problem could be moisture in your fuel system, and this will help eliminate that as a problem. The other thing I would try is to do a Seafoam treatment on the car. If you're not familiar with it, just google "seafoam treatment".
When was the last time you did a tune-up on this car? Fresh plugs, cap, and rotor can do wonders if it's been a long time.
But by far, the best advice I can give to you would be to register on the prelude power forum
Honda Prelude Forum : Honda Prelude Forums. There is a much more active 3rd gen section there. Then seek the advice of a user named TripleLude. He has had a lot of experience working with the carb'd 3rd gens.
Brakes are really not complicated. You said you replaced everything but the lines. So I am assuming you replaced the master cylinder, all four calipers, and all pads. I know you said you bled them, but the only things that could be causing your problem would be a weak brake line or there is still some air in there. If you're sure you bled them properly, then replace the lines. You can get steel braided brake lines from ebay for less than what stock lines would cost from Honda.