I've put the new case together today. I'm pretty much following the AeroVee manual on this, so far it's all very similar. I also used the AeroVee method to measure the shims to set end play. I had ordered a set of 5 new ones but it seems the 3 that were in the old engine fit this one perfectly as well, I have about .004 end play.
The case was sealed with permatex #3 form-a-gasket, bolts torqued in the sequence and to the spec of the AeroVee, cylinder studs loctited and installed handtight. Next come the cylinders and then I should be back where I was before this ordeal.
There is the small matter of torquing the gland nut. I might take the case back to my VW friend to have that done.