To the original poster, how much do you really like the truck? How much time and money you have available for a long drawn out project?
I loved my truck so much that I re-geared, THEN added an E4OD. The E4OD upgrade cost roughly what the truck was worth at the time...and the upgrade was worth every last penny! But it was also a lot of work and more money than most people are willing to spend on an "old beater".
If we're comparing a stock 4R100 to a stock E4OD, the later transmission is slightly better in most aspects, but not by much. As much as I like how my truck turned out, I hesitate to advise anyone else to go through with it on the cheap. If the transmission has known history, and preferably with a Ford spec rebuild, then go for it. If its some used setup with unknown history...might be better off with a 5 speed swap. An E4OD/4R100 upgrade is not likely going to be as cheap as a 5 speed, and if you can't rebuild it yourself, you could be in for a world of hurt later on.
As for the control system, I personally prefer the aftermarket setup. I'm running the original Baumann TCS, and aside from one wire coming loose in the harness, it has been flawless from day one.
One final word of caution on the 4R100. The torque converter won't fit the IDI. The PSD converter will use 6 studs, while the IDI uses 4 studs. So you'll have to buy a torque converter, or try redrilling your flexplate. And you will need to take the starter ring (AKA "Adapter Plate") off the PSD engine block as well. The IDI adapter plate has the top two bolts offset above the engine block, while the PSD is only a straight through spacer (smaller).