Grinding noise coming from manual transmission in 3-5 gears?

Check for heat shield rattles on the exhaust system. This can be erratic in nature and may come across as a rattle, buzzing, or even be construed as a grinding sound. This is often mistaken for a transmission problem too.
Wrap a rag around the end of the tailpipe and whale on the rag with a balled up fist or rubber mallet. If you hear a rattling sound then there’s a strong possibility you are hearing a heat shield rattle.

I think it’s a big mistake to consider taking the transmission apart at this point in time.
There’s a lot more to disassembling and reassembling (knowing what to look for, special techniques or tools involved, etc) a manual transmission than you might think.