2007 Felt B2 Seat Position
I don't think I'll be able to help, but maybe add my experience with a Felt S32 I got. It's a size 60cm (I ride a 63cm road bike) and I have yet to figure out the best seat position. I feel cramped, as you do on the 54cm bike, and I cannot generate the power I can on my road bike; I have contemplated a longer seat post to get my legs a bit more stretched out. With some experimenting, it seems I might also have to raise the stem.
I suppose you wouldn't have those problems when you're trying to choose from a 54 or 56, but I think if the 56 can work for you you might be better off. Have you tried the 56cm bike with a more forward seat position? That might feel more cramped (but less so than the 54), but you'll feel less stretched out in the front.
The 56 B2 also had a 110 stem on it. I could put a 90 on it and I bet it would be perfect.
Well I went with the 56 B2. Apparently I have a long femur which make me tough to fit. The fit of the 54 would put my knees to close to the elbows and make it harder for me to breathe. I have good back flexibility so I can be slightly stretched across my back.
I hope that works out for you. I'm waiting for some warmer weather to do a fitting and/or try some new seat posts.

Anyone riding a 2007 felt B2? If so what size and which seat position are you using? I am looking at a left over 2007 Felt B2 at a shop that is a 56 and a new 2008 B12 that is a 54 at a different shop. If I use the rear postion on the 56 I am too stretched out but in the front position I seem to be ok and I feel like my legs are using less quads. On the 54 in the rear postion I am using my quads and the bike fits ok and I am not too stretched out but then in the front I am saving my quads but I am way too cramped. Any opinions?
The bike fitter is sort of leaving it up to me to decide. He feels I would be good on either depending on my legs. I am new to tri bikes and they are alot different to fit than a road race bike. I am looking for some advice on this one.