To answer the specific questions, no wiring changes needed to accomodate, the reason to flip is actually because in the Mustang orientation the butterfly opens the other direction and the motor is on the outside. Plugs are the same though.
I replaced mine due to the same issue on my stock TB. I was leaking crazy boost from a blown seal in the stock unit, along with the adjuster screw dryrotting and causing a leak as well.
While it offers no performance benefit that I've seen, it is a much better built component.
Even as a dealer I couldn't justify the cost, but managed to find an "open box" item on eBay for $120 so I snagged it. They then lost it and sent me a brand new one for the same price, so it worked out even better.
Hope you get your issues taken care of!