Help with building a 3 Phase DC Motor Controller
As this is not yet homework but going to be, I'm not entirely sure how to answer.  But as a Computer Engineering graduate with several years experience using industrial 480V Variable-Frequency-Drives (VFD's), I would advise you to read the manuals on a few of those.  Try to get multiple models from multiple manufacturers and glean what you can about the inner workings.

There are some tricks that they use that may surprise you, one of which is how they produce an effectively sine output using the transistors as binary switches.

My advice for a general architecture would be to make a basic circuit that is pretty well bulletproof, but only when operated correctly, then do most of the work in software that both ensures correct operation and does the higher-level stuff like position/speed/acceleration control.  And hang sensors all over it; for a prototype, it's better to not use a few than to wish you had more.