This has all been covered a bit in different places but I'll take a shot at doing it here in one place. Our intermittent faux winter this year finally arrived just about the time I got mine installed. So I've only got a little over 400 miles on the bike since it was installed. First impression, however, are that I'm surprisingly pleased with the system. Will cover your questions (somewhat) ad seriatim:
how do ya like it now: The system seems to work completely as advertised and expected. A dyno run tracked the AFR quite accurately to to what the autotune settings were set for.
change pipes or bungs on your existing exhaust: Bungs on my pipes. $10 for a pair of bungs, and 20 minutes using a hole saw, ball peen hammer and dragging out the welder didn't justify the cost of a set of pipes. Plus no concerns about "would it fit?" Just pick and ideal spot and stick 'em on. No problems at all with the install.
Routing the wiring: Still eyeballing after a ride to make sure not getting any chafing anyplace. But so far it has looked as if that shouldn't be an issue. Rear sensor comes back strapped to the starter bracket, under the frame and comes out to the ECM area under the battery box. Straped down to a vertical frame tube and keeps good clearance from the swingarm. My front sensor did not go under the tank. Out of the pipe, strapped that little cross support piece between the downtubes, then down the right downtube, runs along the tube joining all the other harness and line running along the inside of the tube and meets the connector from the autotune module just forward of the transmission.
You wrote that you were considering the unit since you were close to Zippers. Just the ECM by itself I personally would never do unless that were the case. No two bikes are ever the same. No one (ok, almost no one) but them can tune that ECM. Since I could never get it actually tuned to the bike I'd choose not to use it. Just among the population here there are too many stories of close not being good enough.
With the autotune package, however, it is proving to be a very slick package indeed. The setup after installation is straighforward and obviously laid out in the cheat sheet they send. After that's done the system "just works." So far anyway I've found nothing to knock it for. From me that's pretty high praise.