1989-1991 should have a speedometer cable style tailshaft. I read that some later models might still had the same tail shaft internally but the outside casing is blanked off. Best to look for an older transmission to avoid issues here. Note that almost all of the updates for the 4R100 will fit the E4OD. The older transfer case can also be installed on a newer transmission, if 4wd is planned.
ASTG makes good manuals for overhauling and updates. There are two separate manuals: Overhaul book (blue) and the update book (green). I recommend buying and reading through both before attempting an overhaul. YouTube also has several channels that documented the E4OD rebuild quite well over the years.
I've gradually changed my mind on shift kits over the years after seeing how they work, and the effect it has on the transmission. Personally, I'd rather wear out a clutch pack than wear out or break hard parts. There are certainly some updates that the aftermarket offers that are worth installing. But a mild shift kit is usually the most anyone might need.
Sonnax makes some great fixes for the E4OD and I'd recommend most of them. The main updates I would focus on are the OEM ford fixes. Put those in, along with a big cooler, and most of the E4OD's problems go away. If you need to tow heavy you can install more clutch packs and get higher torque capacity, without having to run higher line pressure.
I say that as someone who never drove or owned a stock E4OD, with a stock control system. From what I've read, the electrical systems can cause issues as they age, and it's not always clear what went wrong because of how basic the OBD1 setups were. I still have the original Baumannator TCS for about 15 years now in my truck. There are some limitations to what it can and can't be programmed to do, but it still works.
I might upgrade to the newer US Shift setup, because it has more options for programming the torque converter logic. That was my only real complaint with the original Baumann TCS.