I'd just like to say that everything is fine now.
I left the "other" tone pot as it is due to lask of nesseccary tools and the fact that it doesnt bother me very much.
I ended up slightly lowering the bass side of the HD and raising the treble side because under high gain the bass could be pretty overwhelming. It sounds excellent now and the cleans are even better than before and the distorted it sounds just as good.
The volume drop is actually some sort of short in the toggle switch. Occasionally when the switched from the neck pickup to the bridge pickup the result is that it is still using the neck pickup the volume has dropped by about 80%.
It looked like the wires were literally getting creased in the cavity on the way to the pots cavity so I slightly rotated the positioning of the toggle switch and the problem seems to be almost completely solved and has only occured twice since then, which i fixed. It used to happen very consistently.
If i do see that is come back, though, ill get it properly fixed. I wouldnt want my sound to short out during a gig.
Anyway, I'd like to thank everyone here for all your help and advice. It really helped me keep calm about the situation and solve it.