You can make anything happen if you try hard enough but you cant get much bigger on the stock wheel without getting creative. If you want much bigger than stock you'll have to get taller shocks and I think a fat rear wheel and taller shocks would look pretty lame but thats me. GS550 cast wheels are a direct swap. 16" in diameter instead of 15" but you cant get a fatter tire on it than you can stock. Tech section has a how to on a "much larger rear tire" but you'll have to fiddle with axle spacing and Im not sure if the wheel/rim was stock or not.
As far as the tank goes...yes you can do it...again it requires creativity and probably some welding. Maybe a different seat/mount as well.
Running a straight pipe with no baffle tends to burn up exhaust valves and it'll run like crap and be hard as hell to tune. Get some jets instead and do it right. If you want louder exhaust you can take a muffler off a Harley dyna and shim it to fit the stock header then clamp it down.

I'm 6' also and I am mostly comfortable on my bike. I did move the handlebars back and down just a little bit. I would like to lift the seat some, and if I go with a bobber style seat, I'd try to move it back. I'm also looking into the intruder shocks. Although I'm a bit confused as to the year of shocks to get. Serowbot probably knows the answer to this question. If he doesn't see this post, I'll create a thread asking about it soon enough. ( However, longer shocks won't really change the distance to the controls, just gives a better ride. )

I'm 500 feet higher in Cheyenne, and a Harley Dyna or Sportster take-off from eBay or the local Harley dealer will get rid of the sewing machine sound without alerting the police and irritating every neighbor when you start the bike.  Pop the cover off the air screw as shown in the Tech Section, turn the idle up higher, adjust the screw per Tech Section.  then turn the idle back down.  Some of the gas smell will go away, except on hot days or when you overfill the tank and the soon to be if not now leaky gas cap backflows.  It is running rich, as you might expect from a bike that was set up a little lean at sea level, but is still too rich for altitude.  The Dyna or Sportster muffler leans it, since either is less restrictive than the stock muffler, but then you have to follow the instructions in the Tech section to re-jet.  
A 140/90 rear tire fits if you don't start adding things like bags with bolt heads that stick out.