1.9D Rabbit

[VWrabbit317]

  That's kind of a franken engine.
 Looks like the pump is from a 1.6 right guys?
 I haven't actually seen a 1.9 pump.

 You need to pull the intermediate shaft out and take a look at it.
 Those lines on the back of the belt are left by the I-shaft pully.
 Check the I-shaft bearings and change the seal and o-ring.
 Pull the vacuum pump to support the other end while pulling it out.

What exactly am I looking for when pulling out the I-shaft? Sounds like I’d need to pull the engine to pull the I-shaft, am I right?

EDIT: Once the timing belt is off, can I just grab the I-shaft pulley to see if there's play/movement in the shaft to tell if the bearings are bad?

[ORCoaster]

Can these studs be reused or is it not recommended?

Yes they can and that is why you buy them and throw those old head bolts in the can.

[fatmobile]

 You can pull the vacuum pump and support/guide that end
 while you pull it out from the other end far enough to take a peek.

 There isn't normally any side to side play.
 The bearing chips out in pieces.
 Easy to see with the shaft pulled out a little ways.
 And yes you have to at least lower that end of the engine very far to replace those bearings.
 I prefer to pull the engine to change the I-shaft bearings.