I just rebuilt my t5 and i didnt mark the synchro hub/internal assy.
Anyways, it upshifts like a dream, but if i try to downshift to second it gets stuck, wont go in and i have to go "halfway" (get the slider gear to the 1st gear synchro rings but not the gear, then put it into second, but if i dont really man it in there, it pops out sometimes. its actually been getting easier and smoother as i drive it, (breaking everything in i imagine) but i imagine next time i rebuild it, which will probably be in the next 15k since its not 100%, ill probably need to buy a new synchro hub assy. ANYWAYS, when you do rebuild your tranny, if you do it yourself, or have someone else do it, your probably only looking at about 225$ in parts. I got all new synchro rings, all the small parts, shims washers/snap rings, and bearings for 160 on ebay from brenspeed, and bought a new second gear (ebay) from remanexpress for 57$. You may not need a new gear, but from the sounds of things you may, once you (or whoever) has it apart you will be able to tell.
Good luck.