Mike's a good guy, he won't steer you wrong. I've sold him a tire and cut subframe plates for him. He's a pretty handy guy so I'm not sure why he didn't/couldn't pull that off. LOL.
The wolfman racks are very nice, sturdy, very well made. I personally think with the expedition bags on they're kind of wide, but it's a sturdy and waterproof setup.
I have Dirtbagz and they are not nearly as substantial - the bars will bend if you lay the bike down. but they bend back, are lightweight, easy to remove, and much narrower. Plus they are half the price which I like because I'm a cheap bastid.

I have at least a couple of thousand offroad miles with them and they've been just fine. Dirtbagz are not waterproof which has not been an issue for me in so-Cal. When it rains I stay home. LOL.
Doing it over again I would get a Giant Loop Coyote and keep the Borrego rack for a fuel pack. I like to haul water in a dromedary bag in a rolie bag on top of the fuel pax. I may still get a coyote as it looks like I'm keeping the bike at least awhile longer. There's nothing like it out there. Well, maybe a 690, but twice the $$ and more trouble than their worth.
I don't know enough about the power commander to say. I would PM DynoBob. Seems to me after all the testing and dyno work and all the ways to tune these things, the iBeat was the cheapest and easiest.
Synthetic oil won't hurt the bike - can make seating rings take longer. Just keep an eye on oil consumption, it should be nill anyway. Most of us like to run a dyno oil for a thousand miles or so and then switch to make sure the oil rings seat well. I just don't think it's an issue. And you don't have to have a 'dealer' do your maintenance to keep a warranty in force, you just have to follow the manufacturers recommended maintenance specifications. Hiflo or K&N oil filters are cheap and easy to come by. There was an updated version for this bike, make sure you get the right one. HF563 on the hiflo if memory serves.
If the power-up has been done to the bike it will run fine, just not make the kind of power it will with a proper tune. It won't hurt it any, they just tend to run lean over about 5K rpm. It will start easier and run stronger once you decide on a tune method and get it done. If the O2 sensor is still in and connected then get a PU and at least do that -sooner rather than later. Stock - as built - they are WAY too lean. I bought my PU kit from the dealer when I bought the bike new, and put it on the bike before it was started.
As far as longevity, I doubt they will keep up with the BMW/Rotax mill. Those things are bulletproof. I just don't know of any of the huskys with over 50K miles on them. Seems to me someone posted recently with a rebuild going on at about 50K, barrel was still good but trans gears and shafts were worn. The clutch spring washers need to be replaced by 10K, and keep the countershaft/sprocket mating surface greased as the counter is just held on by a clip and can wobble a bit and wear on the shaft splines. Grease it when you lube the chain. I took the plastic cover/guard off mine, do that on all bikes as a matter of course, just so I can see what's going on in there.