I disagree, here is why;

then they put it together wrong to get it out the door.
Measuring protrusion allows you to determine if someone previously installed the wrong gasket. I've seen quite a few people do it, including VW on their $6500 reman engines.
It also lets you see if any rods have been bent in a bad headgasket or valve crash lockup event.

Valid points, though I think that is more of a concern if you are looking at a 3-notch HG, seems like that's what folks do when they want an easy way out. If it's been running around so far with a 2-notch gasket and nothing bad has happened then chances are that's fine for it, and decent likelihood it is original...

Agree there's no downside to measuring and confirming though, in theory; only argument against is that it adds time and takes some special equipment. Trying to make the measurements halfassed with improvised/wrong tools and potentially getting wrong numbers could have worse consequences than not measuring and just using what was in there already. But if done right, it can only help...

I thought I read on here somewhere to replace the head bolts with studs. Was that correct and are these available from the dealer (Volvo or VW)or aftermarket?

I never put the TTY bolts back in, used or new. I always use studs when I have the head off, heck I have installed studs in three engines without any reason other then insurance.

ARP is the brand I use, I believe there is also race ware?
If your interested in studs I can supply you a set of ARP's for $285.

Regarding the vac pump, setting engine to tdc helps get it back on. Taking it off, at tdc prevents the inner spring launching the pump across the engine bay.

Thanks that's what I did. I had a leaky valve cover gasket so I wanted to replace that anyways. Set the flywheel first, checked the IP notches. First time I've taken the cover off to see how this machine operates. Replaced the O ring on the pump and doesn't seem to be any noise coming from the pump. I checked the valve clearance and it was right at the minimum. Now I'm going to change the injectors to see if that helps the knocking noise. Don't think I can get 5 or 6 unless I move the IP? I will have to get the timing tools first and play around with that.

If you can get the top of the injectors off on 5 and 6. You can get a deep socket over the body of the bottom of the injector.
Otherwise I found it easier to take the top off the pump. Just make sure you note how many threads are on the idle screw and fuelling screw. There's a spring to disconnect on the throttle linkage inside too. Access is so much better after that.

I'll give that a try this weekend. Can you still put the new one back in as one piece?

Hmm, I would be cautious about both of those methods, risk for losing parts, contamination, etc. Especially on the turbo pumps (which are the ones with this access issue) it can be tricky to get the top of the pump back on, even more so if you haven't done it before and your first attempt is with the pump on the motor, not on the bench where you can see everything more easily.

If you scribe marks very carefully on the IP and its bracket, you can loosen the four mounting bolts and rotate the pump away from the motor, get the injectors replaced, and then very carefully put the pump exactly back where it was. You need precise marks for this to go well -- rather than a scribe you may be better off giving a tap at the joint with a sharp chisel or other more exact method -- but if you get it back to where it was you'll be fine. Less risky than trying to count turns on the IP setting screws, and as you noted, disassembling the injectors to get them out doesn't help you get the new ones back in, not to mention the risk of losing the small pieces that will come free when you open the injectors up.

Alternatively you can permanently solve the problem by rotating the pump further out, fixing it in that position, and retiming the position of the rear belt sprocket on the cam, but that requires the timing tools and more work.

Got it, thanks for the heads up!