Do you plan to turbocharge this thing? How much do you want to spend? You can easily pass $1500 in parts alone.
If you are doing this build yourself, I highly recommend getting both ATSG rebuild manuals; The rebuild book itself (blue), and the update book (green).
Rebuild:
https://www.atsg.us/atsg/e4od-1.html
Update: ....hmm can't seem to find a paperback version right now, but it looks similar.
^both of these appear to be available in electronic form if you don't mind getting a CD instead of a book.
You're also going to need some special tools to properly take it apart and put it back together, but if you can cut and weld two pieces of metal together, you can make them from scrap.
Specific upgrades:
For the ultimate, you want to upgrade it to
1995 HD spec or newer in terms of hard parts. That gets you a better input shaft, overdrive gear, forward gear and reverse gear. Older builds all have 3 pinion planetaries with aluminum carriers, while newer ones have a minimum of 4 pinion planetaries with steel carriers (f150 applications may still have 3 pinion). 1993-1994 also introduced a roller bearing center support to replace the undersized brass bushing.
Changing out the front pump to an "F5" (1995 up) will increase fluid flow capacity.
Depending on the amount of torque you anticipate from any future engine upgrades, you can also add extra friction elements to the clutch packs. Exotic materials are also available if you want to spend even more on clutches.
A good quality torque converter is highly recommended since the OEMs are crimped together and tend to explode, sending shrapnel through the transmission. Good quality aftermarket are welded, or brazed. Converters with a billet front cover and 3 clutch packs are usually overkill, but won't hurt. Most upgrade converters are built to this spec anyway since that's what most people want.
Shift kits are ok, but there are three basic types to consider:
1. Electronic. Products like "Banks trans command' simply increase line pressure electronically at the EPC solenoid. This puts more strain on the seals and pistons in the hydraulic system. Not a big deal on an upgraded transmission, but older spec factory builds are prone to cracked pistons on some cases. The converter lockup clutch was known for this (dreaded code 62).
2. Springs & spacers. Same as above, in that these simply increase line pressure. Instead of being plug & play, you will have to drain the trans, drop the pan, and pull the valve body. The advantage is you can tailor each shift individually.
3. Drilling Orifices. This is the most intrusive, but also the best IMO...if done correctly. This method allows you to increase flow to spool valves, accumulators etc. only without having to increase line pressure. The advantage is quick shifting without adding more strain on the hydraulics. The disadvantage is you can't easily reverse permanently drilling a new hole in the valve body separator plate, or in some cases, the casting itself.
But do you need a shift kit?
Keep in mind if you were to add extra frictions to the clutch packs, your surface area will be higher, and it will end up shifting faster from that alone. I went from a 2 element to a 3 element on my overdrive clutch pack and this became the most firm shift. Its a balancing act. So too quick can be more damaging than mushy shifting. If reliability is your main goal, than a firm nudge is all you want. Anything harder, and you're simply putting shock loading on the system.
