I am currently converting my California to 2.5 quad cam ( water cooled already so easier than your task ) Im a few weeks behind your progress as well.
A couple of things that you may be able to help me with, have you got any pics of the thrust bearing assembled onto the primary shaft, I cant really work out where all the clips etc go ... I have looked at the CD from Richard but Im a tad confused !

Also, did you use any gasket sealer between the RJES bell housing and the VW trans axle ? from your pics I dont think that you did...I would always be inclined to add a touch of Hylomar or similar , but perhaps others ( you included ) feel that its unnecessary ?
What are you going to do about the exhaust ??
Regards
Martin