A few notes to add now that the engine is in:
I didn't realize until I had the engine installed that the brake vacuum line and intake were different between the two engines. The new engine had the single vacuum connection at the left front and a built in resonator in the intake line. The old engine had a 3 connection vacuum line with a venturi and a clamp on resonator. I wish I had noticed that before I installed the engine.
Part #21 (Venturi tube) vs the elbow # 23 in the lower picture.
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#23 (Elbow)
The rest of the vacuum tubing was brittle. Probably a good idea to plan to replace
all of it. I missed one piece and of course it broke when I was installing the engine.
After I got it all in and started it up it ran like crap.
Lots of bad scenarios came to mind of what could be wrong. First guess and least scary was MAF and sure enough that fixed it and it was easy enough to do with the engine in.
Differences from the Tiptronic to 5-speed engine:
The wiring harness for the tiptronic integrates the transmission bundle with the engine wiring. There is one vacuum line that splits into a 3 way on the 5-speed that is a 4 way on the tiptronic. There is an extra junction in the cooling lines on the tiptronic that facilitate the transmission cooler. Other than that everything seemed like a direct swap.