handheld tuners

I have a hypertech and I love it. It never messed up anything, but I don't have an automatic either.
We were at the drag races about a year ago and my husband let some guy borrow it. He had a heavy (huge sound system) 2000 Mustang GT Convertible. He was hitting consistent 15.0 or 15.1's in the quarter mile. The car he was up againts was a cadillac cts or something with a northstar engine that was hitting consistent 14.9's.
With the hypertech, the convertible GT hit a 14.8. Needless to say my husband won some money out of the transaction.

Transmissions could break due to other causes such as putting it in nuetral and reving the engine then dropping it into drive (happened to a friend of ours).

I really like SCT. They are a spin off from Superchips - Superchips Custom Tuning. Check them out at www.modulardepot.com. Rather than a generic tune, you get a tune that is customized for your mods. I'd really recommend gears along with this however. Gears will give you the biggest SOTP kick. Buy only FRPP (Ford Racing Performance Parts) gears. And for an automatic, I'd go with 4.10s...at least. Expect to pay about $180 for the gears and $200 for labor. Check around at a local speed shop.
There are plenty of people firming up their shifts, and I'm sure there are a few people who encountered problems in doing so, but I wouldn't let this worry you. Actually firmer, quicker shifts are easier on the transmission...harder on the rest of the drivetrain, mind you...! But, easier on the trannie.
Bottom line, I would go for it.
In addition, this helps me answer your 1st post about the C&L MAF...since you don't have a perf chip or tuner (yet), the MAF probably isn't hurting anything. But rotating the MAF won't help either, since the airflow is straight into the MAF, not coming in at an angle.
Best of Luck!