Well, today was one step forward and two steps back. I spent the first half of the day running all over town trying to find some M12x1.25 socket head cap screws, only to find out that was the wrong thread pitch and I actually needed the much more common M12x1.75. Once I had the correct bolts in hand I was able to install the adapter plate on the engine, along with the crank spacer, flywheel and clutch.
A brief test fitting of the engine in the vehicle revealed that both frame side motor mounts needed to be cut off to even get the engine close to the transmission. With the mounts cut off I could get the engine pretty much lined up with the transmission, but several of the bell housing bolts turned out to be the wrong thread pitch. I'll have to make another trip to the hardware store tomorrow morning.
Despite the new adapter plate being almost 1.5" thicker than the old one, there is not enough room to fit a downpipe between the turbo and firewall. Hopefully there is enough space in the shifter holes in the floor to move the transmission forward another inch or so.
In addition, the power steering pump has almost 3/4" interference with the frame when the crank pulley is centered, so I'm researching various other TDI accessory brackets to see if there is one that fits everything tighter against the engine toward the bottom. It looks like a BEW bracket might be just perfect, will need to take some measurements on one in the morning. I'll also need to get a different intake manifold, I was hopeful that the rear-facing manifold would work but it puts the charge pipe right where the heater core outlet is so it will need to be swapped for a forward-facing manifold. If necessary I can steal the manifold off the old engine for the time being.
At this point I think the game plan is to shift the transmission forward, by 1.5" preferably, then build motor mounts to locate everything in the engine bay. Once the mounts are in place I'll know exactly how much space I have to work with for accessories and can get the appropriate bracket.