it can be moved a few millimeters in any direction, regardless of how many bolts I put in the holes. How do I correct for this? I assume that I'll need to just decide on some method of lining it up for both halves, write it down, and follow it when I put it back together.

Sound kosher?

from the extra manifold you bought as was suggested in the early IMW post? Is your gasket green or gray?

Worst case you can lock it in place with a few well-placed VERY tiny dabs of silicone sealant the size of a pin head long enough to mark each side. I plan on using silicone upon re-assembly anyway as it doesn't hut anything and used lightly it's a great hedge against leaks.

the upper half and put them in the lower half or vice-versa.

You can see them here in the upper left corner and lower right corner. The gasket pictured is the aftermarket "gray" gasket. I have a green gasket for my IM if I ever get to the workshop.

<img src="http://audi12v.home.comcast.net/pix/tdlim/tdlim1.jpg">

Here's another pic, you can see it on the right of the IM:

<img src="http://audi12v.home.comcast.net/pix/tdlim/tdlim3.jpg">

possible the pins are bent a little so are loose?