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?
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.
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.