As far as the chip I'd say it's an option to get the speed limiter removal. You CAN get the Hypertech with the speed limiter removed on it as far as I know but I'd bet it's an option. So you are missing either the Reset button or the Trip/Odometer button? That sucks. Probably can't even get a new button by itself. Have you tried to get a replacement button? You could probably send the chip to Hypertech and have them remove the speed limiter on the chip. They probably have email and it probably wouldn't cost much to have them do it.
As far as the tranny I'd let Ford or a VERY reputable shop do the work. I saw my 96 GT's 5-speed apart and man it's freakin' complicated. I try to do everything myself as well, but personally I'd leave the tranny to the shop. I had a part break on my 1-2 shift fork in my 96's T45. Ended up paying about $1100 after all said and done. Got totally ripped off by a shop and ended up taking it to Ford and getting it done. If I would have known I was going to spend that much I could have gotten a brand new T45 for $1000. Go figure
. Good luck.