Update.
I had another look for the clunking noise.
It happens when I go from drive to reverse or when accelerating and decelerating in 1st and 2nd.
I had it up on the stands again and it appears to be coming from above the diff housing. I can't see sweet fa up there even with a camera. The new diff bushes are fine though and everything is done up tight.
The control blade bushes are totally farked so I'll swap them out and see if the clunk persists. Obviously the clunk isn't coming from them but they are allowing a couple of inches of play.
If it does persist I'll drop the subframe again and replace everything in it.
I tweaked the tune slightly and had a positive result. I've recently just started to pick up a misfire after extended load so I'll be looking at the plugs and coil packs and checking they're all good as well.
Fun, fun.