Andrew, I read your FAG
http://www.vwdiesel.net/forum/index.php?topic=18464.0 but it is unclear if the Intermediate shaft bearings can be R&R'ed without engine disassembly.. I just got back to working on mine, pulled the timing belt off and checked all the sprocket shaft bearings and found the Intermediate shaft had a lot of movement (I can hear it click as I rocked it side to side) and there were lot's of oily gunk all over. This is probably the source of the high frequency squeak that I was trying to identify. I can make the special tool in your FAG no problems but the question is : Can the bearings be removed and replaced without disassembling the engine? Do I need special tools to pull the bearings or will your tool also do that? This car has been a nightmare, will it ever end?
ok so I missed that. What else has to come off first to remove the intermediate shaft, oil pan and oil pump? Any special tools required?
I got the IS sprocket off and there are 2 botls that secures a cover for the shaft. Oil pan is clear of obstructions. Damm I just changed the oil.

Interesting that the shaft only has play and clicks when moved side to side and not up and down. can you explain that? I am inclined to just replace the seal on the shaft cover/retainer and put it back together and check oil pressure and oil leaks. Can I run with the upper and lower timing covers off for a few hundred miles so I can spot leaks easily?
Can anything become dislodged if I pull the shaft out? How far should I pull it out? Is there any chance that I will not be able to push it back in? The seal don't looked that bad. Not deformed with a smooth seal surface (per my finger). Since I do not have a seal puller I am leaving the old seal.
Andrew? I am waiting for your valuable input to my question above before putting it back together and slapping a new timing belt on. Running with no covers is only temporary. I will take precautions and put a bottom plate to protect the T-belt from road hazards
Can anything become dislodged if I pull the shaft out? How far should I pull it out? Is there any chance that I will not be able to push it back in? The seal don't looked that bad. Not deformed with a smooth seal surface (per my finger). Since I do not have a seal puller I am leaving the old seal.
There's a bearing on both ends of the shaft, just pull the shaft out being careful not to let it clunk down when it comes free of the bearings, to install it you might have to turn it as it goes in to align the vac pump gears.
You don't need a seal puller, a screwdriver and hammer will work to get the seal out and the right size of socket and will work as a seal driver.
I wouldn't run without the lower cover for sure.
P.S. Changing the bearing is no fun, I did just the outer one and it gave me the fits, do a search and you'll pull up lots of info.