Don't get too excited about Fluids based on Chem and thermo. I also loved thermo and chem, but Fluids was not my cup of tea. Do they offer any Combustion classes at your school? They generally are taught by the chem department, but they are fun. I would also suggest taking a turbines class if you like Thermo. Mach theory is pretty freaking cool, then you can apply it by getting into jets!

Back to the subject though, was this the plane that you mounted the .55 on? Do you think that might be causing issues? Added weight, but added thrust will most likely make your plane change dynamically over a range of speeds. If this is the plane with the .55 and if they recommended a smaller motor (.40-.46), maybe you might want to try putting your .46 in it and seeing how it works. with the added thrust of the .55, that might explain why you might need to increase your down thrust of the motor. It might be pulling the nose up too much.

If this is not the case, then disregard. If it is the case, look at it this way. Think back to your statics class and think about it this way. If the motor shaft is not mounted inline with the wing chord and the stab (like a stik - they are closer than most planes), then you are creating a bending moment when you are creating thrust with the engine, because the drag of the planes wing (being high) will try to pull the plane back, creating up AOA. This is partially overcome by adding downthrust to the engine mount. The faster the airspeed the higher the drag (drag increases proportionally to the square of the velocity).

Don't give up, but like Nathan said, isolate, isolate, isolate. It's like deconstructing a problem in school, you can do it, just stay with it.
Regards,
Curtis
P.S. Of course this doesn't explain why it might fly different than before the crash. However, if you got the engine running better now, then more thrust.