ol' yeller wrote:
Rough running on that vintage V10 could also likely be one or more bad coil packs. The rubber boot around the coil pack deteriorates and cracks with age and lets water down around the plug and shorts out the coil.
To add, the plugs are down in a well in the head which holds water remarkably well depite the high temps under the hood. Also the V10 runs remarkably well with several plugs misfiring.
Usually tranny problems would be things like slipping or mis shifting.
Go to your FLAPS (Friendly Local Auto Parts Store) and borrow (or rent) an engine code reader. That is the best place to start. You can't mess up your engine using one.