The coils can pass the bench resistance checks, but still be bad from internal shorts that don't become evident until the coils are stressed. A test you can try is to ride the bike at highway speeds, then stop & feel them to see if they are getting hot to the touch --- press hard w your fingers -- they should be warm, not hot. Mine were getting hot, even though they passed the resistance checks. Also, the old spark plug wires may not be as conductive as they should be. I guess the spark plugs might indicate if there's poor ignition (?), so you should check their color.
To do a muffler patch, roughen the chrome. okc-kent roughened the area & scored lines in the surface using a dremel, giving the adhesive something to grab ahold of. Too bad the patch photo is gone -- it was really nifty looking, since the ss shined up almost like chrome. The patch was quite a bit larger than the holes, probably so he'd have surface area for the adhesive. If you decide to use a patch, I would use 4 small ss machine screws & I probably wouldn't bother tapping threads ---- just drill 4 small holes & install the screws.