[v8volvo]

IMHO that would getting ahead of things a bit -- those concerns are possible, but there are ways to protect the bores (and oil passages, water jackets, etc) from intrusion of contaminants while working on the bolt holes, and you can probably clean up what's in there now by running the pistons up and down a few times with oil in the bores to catch whatever the rings push up, shooting in some air at TDC, etc. Disassembly of the bottom end is definitely not a routine necessary step during a headgasket replacement, much less honing bores.

Provided you don't see evidence that bore damage has occurred already, I think I would probably try to put a limit on how much work I commited myself to, and leave it whole unless/until the machine shop says more of it needs to come apart in order to do their work. If you can keep it as a complete short block that you can just plug back in and stick a head onto after you get things sorted out, that's really a whole different kind of job vs pulling the bottom end apart. Personally, given that this work is not being done in a sterile machine shop anyway, I think you would introduce more possibility of contamination by taking the crank system apart than you are looking at now.

My $0.02 anyway, worth what you're paying for it, etc. I guess my main suggestion would be to get the machine shop's opinion, and only pull it as far down as they say you have to. You going to work with All Pro again?