It's been doing this for a bit now, and it only does it for third gear. If I switch from 2nd to 3rd, or neutral to 3rd at 4000rpm or higher, it makes a clunk and a grinding sound. No other gears do this. I recorded a video just a little bit ago, but i forgot i was connected to my bluetooth so the audio was bad. But here it is anyways. It's my first manual car, but i think it may be a synchro? Note that it does not continue making noise while in gear. Only when switching into gear.

 

I could hear it ok. Sounds to me like the sychromesh on third gear is worn. If this is the case, then the wearings will be in the gearbox oil wreaking havock with everything else the oil touches. There's no quick fix I dont think. The permanent fix is to take out the gearbox and either renew it witha second hand one from a scrap car ( cheap method) or ask someone to clean it all out and rebuild it for you ( expensive method). Has your car covered a great distance? or has it ever been driven in a "flamboyant and spirited manner" on a regular basis?

 

I got it back in November with about 153k miles, it's at 160,875 now. I can't really say when I started noticing the sounds, just that I did after a little while. I'm usually fairly tame when driving, but I definitely do have some spirited moments, especially when there are other spirited drivers being spirited.
I'm just gonna take it easy until I come up with the money to fix it I suppose.