I think the problem is your original transmission was having a synchro issue at the 5th gear, which migrated to the 3rd gear synchro. When I say "migrated" I mean that it too is worn out, not that there is an "infection which is spreading". I would venture to assume your new-to-you transmission suffers from the same fate. If you bought the transmission new or used, it should have some type of warranty on it (probably 30-day on a used or 36 month/36k mile if new). Get a replacement for it as long as a warranty is available (obviously if you bought it from an individual, you won't have that option).
I don't think it is anything else you've done, considering the only other thing which could really be causing this is the hydraulic actuator, but you've already bled it. Plus, if it were clutch related, it would have issues in all of the gears and it wouldn't grind. It would just be hard to get it into gear (the exception being reverse, as most reverse gears do not have a synchro).