Sweet swap! I did the same wth my '73 bus last winter...ALH mated to my regeared 002 transaxle. I too have heard the stories of the VW transaxles letting go in short order...but after 9 months, im still going.
In the meantime, Ive pieced together a Passat DUK 5 speed (diesel 5 speed from Canada) & a flip kit. I still need the axles & to sort out shifting (Porsche Boxster 5 speed shifter)
One thing i see on yours is the intercooler location.....trying to flow air through it and into the engine bay doesnt work...I had super high IAT's with this arrangment (200°F +!). I tried a water/air intercooler...which was better...but not great. That with the added complexity of needing anoother heat exchanger to dump the intercooler heat, and a pump...I sourced got a small intercooler from ebay, shoved it in that same corner facing down, and cut a rectangular opeing for it in the sheetmetal. Then I blocked the whole thing in, and isulated it. My temps now are 130° on a 90° degree day. Higher than id like, but the the exhaust temps good, which is where the ruber meets the road as far as this goes. I still might puller fan down underneath to see if this helps. I can post some pics of the set up if you are interested.