Well for any manual swap you'll need the manual pedals for a '92-'96 truck (gas or diesel doesn't matter), then a master cylinder, a hydraulic clutch line (preferred choice is the stainless line for a '95-'96 Powerstroke diesel truck), and whatever slave cylinder your new transmission calls for. Possibly a crossmember for the transmission mount. Definitely driveshaft, the E4OD is silly-long while the manuals are much shorter. Most people go for the ZF5 manual transmission, that one I'd estimate around $1000 for a used transmission and new clutch and flywheel alone, all the aforementioned parts add on top of this. If you don't care much for overdrive gear, or you're on a tight budget, there are the older 4-speed transmission, those tend to be much cheaper than the ZF5. You have your choice of T19 (with three different gear ratios to choose from), NP 435 (has creeper 1st gear), and T18 (also creeper 1st gear). Only the close-ratio T19 was standard behind IDI engines and IMHO it works quite well and is pleasant to drive, but really as long as you have an IDI bellhousing in your possession you can run any of these transmissions with the same clutch setup, basically mix and match till you get what works best for you. The main issue with any of these 4-speeds is the relatively high engine speed they need to keep up with interstate traffic, even with 3.55 axle gears the truck will top out at around 80mph (slower with 4.10 gears), and that's with the engine screaming at 3200 rpms chugging fuel at like 10mpg. At 55-60mph she should pull 15mpg consistently tho.
On the automatic side you have the 3-speed C6, situation there is similar to that with the 4-speed manuals in that she slows your truck down and makes it thirsty at high speeds. But again like the 4-speeds she's very tough and reliable, and fairly cheap as well. There is also the option for Allison automatic, that one will have to come from a school bus or a medium-duty truck, it's a 4-speed automatic but no OD gear like the E4OD, so think of it as a heavier-duty C6 with an extra lower gear. Neither of these transmissions is a very suitable choice for something that goes on the interstate a lot, but for hard work on back country roads both will work well.
Regarding your E4OD question, even if all connectors came unplugged completely an E4OD will still have reverse and be able to move forward in 2nd and 4th (OD) gears. This is a hydro-mechanical backup built into the transmissions, so truck can still be operated if needed in case of emergency. The fact that you got no motion forward or rearward tells me it's not an electrical issue, something important broke inside the transmission. Trackspeeder says forward clutch, he knows these transmissions very well so he's likely correct.
If wheels and tires have unknown history, this is all the more reason to have them checked out.
As for the hub seals, that Timken will work on both 2wd and 4x4 trucks as long as the rear axle is of the Sterling variety. The 10.25 number Jasper mentioned refers to the size of the ring gear (big gear bolted to the differential) inside said axle, it's 10.25" in diameter. Later Sterling axles go ta slightly bigger ring gear, 10.5" in diameter. But your truck will have the 10.25" Sterling rear axle, it's simple to work on and can take a lot of abuse without complaining (as long as there is enough oil inside). Another good seal for it is the Scotseal XL, it's quite similar to the Timken seal in design (and price I think), just different manufacturer.