Lot's of great info here if you haven't found it already:
http://www.gowesty.com/library.php
I disagree that shops are more reluctant to work on conversions. I find the opposite with mine. They all cringe at the thought that there is a waterboxer inside and then they get real curious to pop their head in to check out the conversion. (Just my experience) Most mechanics are familiar with the engines and know exactly what they are looking at.
I have a Jetta conversion. Super simple and fine for a 2wd. Cheapest conversion of all. If I did it again being a Syncro I would go for the big TDI and never look back or subby as a close second choice