Ok! So. We took off the engine covers and the nut wasn't as loose as last time. Certainly above finger tight - which is odd because the noise was a lot worse than before. We removed the nut, added decent loctite and retourqued up above the workshop manual recommendation (as others have done on here). I left the mechanic to clean off the old gaskets and put it back together. He replaced the oil and filter and started the bike and the noise was still there (albeit slightly better).

Apparently Yam TDMs don't respond well to aftermarket oil filters (I've used the readily available Hiflo ones for the past 4 years). He replaced the filter with a genuine yam one and now it sounds absolutely perfect! Either that or he filled the engine with sawdust. I really cannot believe how much better it sounds now. The engine itself just purrs - it's always sounded like a bag of nails since I bought it!