I think I know the answer, but I want a 2nd opinion before I get worried and do something rash.
I fired up the rebuilt 1.6 diesel Golf for the first time a couple weeks ago. Had some issues with gauges, etc... but it started and ran immediately, a little white smoke but sounded nice. I found a coolant leak that I needed to fix, so I pulled the injection pump to fix some other minor things that I couldn't reach- I didn't pull the lower timing belt cover but I had the cam lock tool in place. I got it all back together, and now it won't start- well, not really. It will cough and fire a couple times, and sometimes stay running very very poorly if I press on the accelerator some. It also smokes white a LOT. I put the injection pump back where it was, I do not have any way of checking actual pump timing.
I'm guessing I fubard the timing when I put it back together, or the belt moved a tooth or two on the crank pulley. What sucks is that I don't have a good way to find TDC on the crank, I measured and marked the flywheel but I cannot get the green cap out of the tranny to get a good look at it, plus I figure it won't be real accurate anyway.
Also sucks is that I have spent literally two weekends fabbing and fitting the intake/boost tubing, and now I have to take it all apart to reach the lower timing cover.
So, y'all think it's a timing thing?
Thanks,
Brendan
the TDC mark should be right next to the middle bolt hole. you know, the ones that hold the flywheel to the pressure plate? take the plug out with some rather large vise grips. your timing is just off.
I use a 1 1/16 nut to take the tranny timing plug out. Either that or a chisel and a hammer. Depends how I'm feeling
It does sound like a timing issue to me. Did you have the cam locked?
Yep, cam was locked. Not sure how the timing could have changed but I don't really know what the crank did while I was working since I didn't have the lower cover off.
Brendan
Not sure how the timing could have changed
If you took the pump off the timing changed %100. Moving the pump like ridiculously small amounts affects timing to the point of the engine not running. lol
GET IT TIMED

If all you touched was timing when you messed with it, that is the only reason why it wouldn't run.
You are saying that the pump timing itself can be far enough off that it won't run? I used the locking pin, and put the bolts back in the same orientation.
Or are you saying that the belt might be a tooth off somewhere?
Thanks for the replies. It does not appear to be raining today so I might start to tear back into it after work, for about 15 minutes that is before it gets dark.

Brendan
There is no reason to take off the lower timing belt cover for this operation.
You are saying that the pump timing itself can be far enough off that it won't run? I used the locking pin, and put the bolts back in the same orientation.
Or are you saying that the belt might be a tooth off somewhere?
Thanks for the replies. It does not appear to be raining today so I might start to tear back into it after work, for about 15 minutes that is before it gets dark. 
Brendan
The pump alignment isn't anywhere near as coarse as a tooth on the timing belt - we're talking moving it a mm changes the timing noticeably. The locking pin for the pump gets you close enough that you can PROBABLY start your engine but it definitely doesn't set your timing correctly.
If you don't have access to the proper timing tools (dial gauge with either an adapter for the pump or some other way to measure the lift) and you can get the car started you CAN adjust the timing by moving the pump a bit while the car is running. But you definitely need to make sure your cam is the right place first...
Perhaps the pump is 180deg out
Perhaps the pump is 180deg out 
I seriously doubt it. There is a notch on the sprocket and a key on the shaft, I didn't turn the pump at all when I took it off.
I'm gonna guess that something slipped when I was re-tensioning the belt. I'll hope that's what it is anyway.

Brendan
Muahahahaha!
Fixed it. It was in fact timing. The crank was a few degrees out. I didn't even change out of my "good" work clothes when I got home, just started tearing it apart. Actually got it all done, re-timed it, and it fired right up like it was supposed to.

I think the timing is still advanced a bit too much, the diesel clatter is pretty loud, louder than I think it should be, but it's running and revving really smoothly. Now to pop on the axles, un-freeze the parking brake, and take it for a spin! Hopefully I can get that done this weekend.
Thanks for the advice everyone, and for not letting me jump to conclusions about it being something more serious.

I also took some pictures and I'll update the main build thread here in a few.
Brendan