Doh, that'll do it!
I worked on the Jetta again last night. I hooked everything back up (forgot I hadn't plugged the glow plugs in after testing them) and fired it up and only got check engine lights for the glow plugs this time. This was a problem before the swap, so I figure its a problem with the harness. I did check the resistance on the plugs and one of them is off (about 13 ohms), but the others are fine (around 4 ohms).
The clutch pedal problem was odd. The pedal was just stuck down and didn't fully return. However, once I pulled it back up (with little force) it worked perfectly. Yay, super easy fix.
So, now my final problem is that it won't shift into reverse. I have all the other gears, but not reverse. When you go to put it in reverse, it just goes into 1st (tested by trying to drive it backwards and it goes forward), even though it does go the extra bit over. I had my wife shift the car for me while I watched the transmission linkages. It looks to be working properly but perhaps just isn't moving quite far enough? So, I'm thinking it either needs adjusting or just needs to be worked a bit as it is VERY stiff and hard to move the shifter from side to side. I assume this is just from sitting so long.
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