I've had #770 since October 2000...and NEVER had a header or flange bolt/nut come loose enough to lose one. But...I've had to tightened them up several times before I hit on a solution.
I ended up using all stainless bolts, nuts, and lock washers. Using a 3/8" drive ratchet with extensions and deepwall sockets, along with a box end wrench for the bolt head, installation, removal and maintenance is really easy...no problems at all reaching any of the six fasteners. All the taping, wrapping, and otherwise protecting the body and pipes is really overkill and typical of a new owner, but no problem...we all understand your concerns and precautions. But basically, you're taking waaay, waaaaaay more pains than you need to...the paint and ceramic coatings are much more durable than you may think. Trust me when I say you'll pick up waaaay more nicks and scratches in one week of driving than you'll ever incur while installing your side pipes...!!!
After installation and initial run in, while the headers, pipes, flanges and bolts are still good and hot...revisit each one and tighten them up again. You'll find that after heating them up, you'll be able to get as much as a full turn on each fastener...! The heat obviously makes them expand quite a bit...and this is what causes them to get loose. Tightening them up while hot insures they stay tight when they heat up again. I don't need to tell you to be careful while they're hot...or you'll burn the Bejeezus outta your hand, arm, and anythng else that comes in contact with the hot surfaces...ask me how I know this...!!!
Also, at least once a year, just after a hard drive, again while they're still hot...go 'round and tighten them all up again, or at least try to. The key is re-tightening them while they are extremely hot - just after a drive.
This procedure has worked well for me for the past 8 years...hope it helps you out.