I've done the auto (5R55E) to manual M5OD-R1HD conversion to my 4.0L SOHC.
The R1HD was the "Heavy Duty" manual transmission used by the factory in rare post-'99 SOHC engines, such as the Ranger FX4. The R1 was used for the OHV's.
The two casings are the same, so they will both bolt up to both engines. The R1HD DOES have a lower first gear than the R1, with the other 4 gears and reverse being the same ratio. Other than that, I'm not sure what else is different from the R1, but judging from the "HD" badge, I'm guessing it's built beefier somehow to accomodate the 210hp engine (as opposed to the 160hp OHV).
You WILL have an issue with the computer. The "computer" that runs your engine is the same computer that runs your automatic transmission. So, yes, the manual transmission runs on it's own, but your computer, which is also running your engine is going to get very confused when it doesn't get readings back from your automatic, which isn't there anymore.
I am still using my factory SOHC auto computer, but I had to various circuitry to get the truck running smoothly. Right off the bat, I can tell you that you have to jump the Park or Neutral wires so you will be able to start the engine in the first place. At this point, you can "drive", but I experienced terrible roughness. It's as if the computer was killing the gas at certain points in anticipation of an automatic shift, which wasn't occuring.
I ripped out all the sensors and solenoids from the original automatic, attached them back to the wiring harness in the truck, and simply ziptied them to something stationary (be careful, they get hot, don't get them near plastic). It pretty much ran perfectly at this point except at full throttle.
I then used resistors to imitate the resistance in the original auto to jump all the wires that would tell the computer, "hey, i'm Mr. Automatic Transmission. I'm still here and feeling great. By the way, Mr. Computer, I'm in Neutral gear, so you can let me start my engine AND you don't have to worry about fuel mapping and up/downshifting. I know, I know, we're going 65-mph in neutral, but you're just going to have to trust me on this one."
Your other options, which I can't vouch for, would be to just get a new engine computer designed for a manual. Since you have an OHV it will be much easier to find than the rarer SOHC. Also, if you don't live in auto-ignorant NYC like I do, then maybe dealerships will actually know what they are doing, and can find one for you.
You can also try getting a chip made. I know, what's his name, from Diablo (oh, i forget, the guy who does all the good chips on this board though). I spoke to him once, and he said he'd give it a try.
You won't need a harness. There are 2 electrical connections to the manual transmission. The reverse gear for the lights, and there is also an output speed sensor (i think only on the HD). The 5R55E had both an input speed sensor and an output speed sensor, but I already did the work of counting the gear notches on the output speed gear, and they are not the same, so I wouldn't try hooking up the old wires to the new OS sensor. I just left the new R1HD OS sensor there to keep the fluid in the trans, but left it unconnected. The reverse gear electrical connections aren't the same, so bust out the soldering iron. Do a good job the first time with solder and heat shrinks and use silicon all over the connection so it doesn't rust off. I had to redo this a bunch of times.
Let me know if you have any more questions.
