Good answers all.
[1] Dyno tuning your bike is not necessary if you can find the right tune file for your setup, but if you want the most from your bike then you must dyno tune it and in that you are tied to PCIII unless you can find a Tuneboy tuner in your area. Otherwise, I'd get Tuneboy over PCIII any day.
[2] I used to use the Unifilters and personally don't recommend them. Not only are they a fire hazard but are freekin' messy and ooze oil all over the bike components around and under them.
[3] If I still had standard air intake, I'd be using K&N.
[4] Basically true. Personally, it is not technically "correct" to just remove the secondaries because the ECU fuel maps will not match what is going on. This means you'll run lean at lower throttle settings but probably won't hurt anything at least in the short-term. It'd be best to remove the secondaries and dynotune the bike after so it is all tuned correctly. If you do want to remove the secondaries and not dynotune then I'd recommend using Tuneboy to make sure your secondary maps are all 100% open so the ECU knows about it and matches fuel/air better.
[5] Tuneboy is the only tool that has the actual factory maps, but far as custom maps for nonstock setups, there is no difference because they would all be non-optimal for your bike anyways since they were all taken from dynotuning someone else's bike. So this isn't really an issue.
[6] The clutch plates won't go in 1000 miles but closer to 10000 to 12000 if you're hard on them, which is about half a normal life. I had to replace my heavy duty Barnett clutch plates after about 12000 miles of use or one season of riding for me. If you do wheelies, burnouts, drag launches VERY frequently then I'd expect the plates to go even sooner, probably a few thousand miles.
[7] Not essential but like said, if you want the best from YOUR bike then you have to dynotune it.