That was my project over Christmas break this past winter.
my personal suggestions are to ditch the banks transcommand you'll be able to get better results doing all of the work internally and since you're rebuilding it anyway there is no reason not to do it correctly, Banks uses computer controls because it's easy to install and meets the minimum requirements. And you'll find that the combination of the trans command with a shift kit will not be a pleasant driving experience or so I've been told.
Internals be sure that you are getting all applicable internal upgrades, which (forgive me for only knowing what applies to my E4OD) for me was higher pinion count planets, steel planets instead of aluminum, more frictions in the clutch packs... and the list goes on.
For the valve body rebuild / shift kit (and also a lip seal and a couple snap ring upgrades) pick up the
transgo tugger HD2 kit. It has all of the pieces for your valve body and a complete rebuild, it has a calibration plate to allow you to customize how firm the shifts are, which is very nice.
You mention the trans pan but do you have an auxiliary aftermarket cooler? If not I'd recommend picking one up
Here is a good place to look anything from the 4590 on down on the page will be adequate or look into the 6.0L or V10 trans coolers from Ford.
I like you already had a good converter and was going to reuse it. I ordered the parts from RacerX as mentioned above for a source of parts. Suncoast also has parts kits and would be able to make recommendations on the calibration plate in the shift kit that will give you exactly what you want on the first time since they also use the tugger kits in their rebuilds.
