(I know this is a duplication of the build thread but would be useful for anyone else searching in the future. )
For this to work properly I need to get the engine shaft and the gearbox shaft aligned as best I can, preferably perfectly.

I've borrowed a friends magnetic surface gauge to help me. The magnet is stuck to the cast cylinder fins and the business end is on the inside of the flywheel centre bush I made.

Now in order to turn the engine with minimal force I took the rockers off and removed the push rods so I'm not having to compress the valve springs. I also inserted the bit of wood so the valves are kept open a bit and there is no compression.

The error is 0.006" or 0.15mm. I'm not happy but continue.

Inserting a length of 9mm ground bar the error is now 0.005" 0.13mm.

The clutch push rod is 8mm and the hole is 9mm which is a perfect match for a length of 9mm ground bar which is oddly enough an available standard size. The gearbox slides over the 9mm bar. The flange is held down but not tightened so as the engine is rotated the surface gauge will indicate the error in alignment. It is unsurprisingly 0.005" out
Not happy with 0,005" I took it all apart and back together about three times and after a bit of tapping with the rubber mallet I managed to get it so the surface gauge didn't flinch at all as the engine was rotated

You'll have to take my word on it that this is where the needle stayed!! I'm not saying the thing is aligned with absolute perfection but it s now within the free play in the alignment tooling and spline coupling and I ain't going to get better than that.
After this was achieved the bolts holding the flange plate to the bell housing were very carefully nipped up tight.

After that the gearbox was removed so that locating holes and pins could be fitted.

These are the engineering pins and the hole they go in. They are tapered ones so I had to ream the 6mm hole out with the correct matching tapered reamer.

In it goes....

And tapped home with my smaller hammer = Everything in alignment again

If you look at the photos you'll see that the inside hole of the adaptor plate is circular. It is a little known fact that the locating lugs on the BMW gearbox are circular and concentric to the input shaft allowing easy machining of an adaptor. The correct sized interference hole was turned on a lathe from of a sheet of 4mm steel bolted to a face plate.