Right... time for some updates I guess.
Only small ones atm, I've been doing lots of designing and not a lot of making, but hopefully going to sort out this problem properly. Designed lots of new engine mounts that are awesome in most respects, but none that solve all problems yet. Will get there.
Still, in the meantime, I've been collecting/making parts to put everything back together with. New bearings engine side(spigot, clutch release, bellhousing output shaft) caused some issues, the clutch release bearing seems to be pure unobtainium at the moment. I was about to make up my new version on the 4 axis CNC to take a standard 7206 when 10 clutch kits came up on ebay for not silly money. Grabbed a few of those for now, will make the new bearing carrier when time is a bit free-er.
Same with engine mounts, I could carry on designing for ages, but until I'm sure what to design around it's a bit pointless. So, I rang Dai up and got him to send me some new mounts.
But... I needed some thing to tell me what was going on, as all I had was assumptions. So, I made a new Chris' Special Tool, the CST002.
With Friggin' Laser Beams
The CST002 is a lump of an old torn apart propshaft, where the spliney bit has been removed from the sleeve bonded into the rubber with an eleventy ton press. They are pressed in there pretty well, it needed all eleventy tons and shot across the room. Add to that one laser pointer and lathe up a lump of something to hold it all together (I used PEEK with adjustment grubscrews, as I had both to hand).
The CST002
Then, slide the tool onto the gearbox input shaft and turn the on-off switch (cunningly disguised as a cable tie) to laser-ise

As there is a small amount of run out in the laser pointer that I didn't take out (needs another ring of grub screws) rotate the input shaft to describe a circle, the input shaft is pointing to the dead centre of this. Here you can see where the gearbox is nearly spot on, the break in the circle is the laser being projected on the clutch output shaft, the main 3/4 of a circle is against the bellhousing
So, now to try the other end. This is more tricky, as I havn't yet connected up the clutch, I can't rotate the shaft, but I can get a good idea of whats going on. Currently on old mounts, for a comparison. Mounts mounted half way up the slots (which I never do, just put it in quickly in the dark last night and this is where they happened to be when I looked)

Place on the clutch output shaft

And the point, which could be anywhere on the previously seen circle
Not as bad as expected... high, so, lets put the engine mounts to where they should be.
And where is the point... pretty much spot on... hmmm
So... what can be concluded...
Well, nothing at the moment really, statically everything looks pretty good, I'll hook the clutch up later (I've filed some of the nylon spacers, so need to make some more) and do a circle test engine to gearbox direction.
The next thing is dynamic loads, both times something major has fallen apart has been under very hard acceleration and on stock mounts everything does flap about a lot. So, I need a way of mounting the camera to the car so I can shake the engine without moving the camera relative to the car. Preferably with the engine spinning. Will plan that test when I get another free minute.