[ChrisD]

We got the new diff installed in the end

I got this reply from Kaaz (the makers of my diff):

Most GT86 installs done here required total shim gap of over 5mm.
Normally about 5.3~5.8mm total gap space.
So if you only have 4.4mm, this gap in the bearing is probably causing the shim
fitment issue.

So we had another look and it turned out the reason the bearings weren't going on far enough is because the thing we were using to sit between the press and the inner race was not quite the exact right size for it, despite what we originally thought. It would push it down most of the way but then get caught on the tapered edge of the diff that sits inside the bearing. Once we realised that we found something else and they slid on all the way pretty easy.

Then we put the original shims in and measured backlash etc and all seemed perfectly within spec. So we got it all back on the car and so far so good! There's a very noticeable clunking sound on tight slow turns but apparently that is normal (though its hard to know if it should be quite this loud and noticeable) but no whining sound when driving at any speed at all.

One question I do have is how did anyone else torque the bolts on the drive shaft up to the right torque spec (the 4 bolts that hold the drive shaft to the pinion flange on the diff) ? We could barely get a spanner in there let alone a socket with a torque wrench on it. So we just did them as tight as we possibly could, but always wary of not doing things up to the right torque spec.