Well, while I'm sure anything is possible, I always thought that if you had it power flushed at a shop is when you could possibly screw it up, because that knocks all the junk that is sitting in it loose and it gets stuck in places that it shouldn't.
I changed the fluid in my 95 to Mercon V at about 65K, and it worked fine up until the day the intermediate clutches gave out, which was not caused by the fluid change. This was at 95K when it died. I will note that the reason I changed it out is that I had TC shudder and it solved that issue.
I would say drain the TC, lines and drop the pan. Change filter and all that and refill w/ Mercon V and be done. I am by no means a tranny guru, but I don't see why changing the fluid on a perfectly good working trans. is going to kill it. If anything, by switching to the Mercon V you will be helping to extend the life of the trans. Adding a cooler is always a good idea as well.
Just my .02
Jay