1) Measure twice, cut once.
2) If your new sprockets are the same size as the old, then your chain should have the same number of links - give them a side by side inspection. If the sprockets are smaller, you may need less chain.
3) If you need to shorten the chain and you don't have a chain tool, use a hand grinder to take off the ends of the pins down to the side plate, then push them out with a drift. Easy job.
4) I've never tried to use a chain that was too long, but it should work (in a pinch) if there is enough adjustment in the swing arm slots. 2 links = 1 1/4". Extra length split between top and bottom - wheel will be 5/8" further back (I think, but - too much math for Sunday morning). When the new chain stretches it may have to be cut anyway. Sounds like a bad idea to me. The axle should be near the front of the slots for a new chain and towards the back for an old one. My new chain put the axle just short of the first mark.
5) You haven't mentioned the master link and I don't know what an HQR has. I don't have any experience with riveted master links and you may find that you need a chain tool tool anyway.
6) I use a cut up coathanger to fish the chain over the back sprocket and through the chainguard, and make the master link at the rear sprocket. For clip type link, closed end of clip points in direction of rotation.
7) If you don't trust the adjustment marks on the swingarm, check wheel alignment - that's another thread.
Measure twice, cut once. What's important is the number of pins in the old chain. Don't cut unless you are certain.
I've lost count of how many chains I've put on my cycle. I put a new DID standard chain on this year and cut down from 110L to 100L. I tried an o-ring chain - it might have been the last one I ever put on this bike, but it hit the chain guard so I couldn't use it.