Inspect them for cracks, if they're cracked then replace them or use a section of heat shrink tubing as a repair 'jacket' to prevent the crack from allowing the coil pack to ground to the valve cover or whatever instead of pumping the spark through the spark plug. Often times folks will replace a coil pack chasing a misfire issue instead of the boot, when the boot was actually the problem.
Hotter and drier climates tend to be harder on rubber components like that.
Depends entirely on the tune. For a canned tune from a programmer, just for CYA I wouldn't expect them to disable or limit the closed loop correction for things like knock count, but I've seen some weird shit. If you flash your PCM with an aftermarket tune that calls for 91 octane or better, I'd be fully committed to 91+ all the time no matter what. If circumstances dictated the use of 89 or 90 octane, I'd baby it at part throttle and I'd keep the revs as low as possible.
Glad to hear that my old hobby-turned-profession experience is helpful around here