Tricking the PCM
Don't know if you solved your problem with not being able to shift into 4L by now; but here is how I solved that problem on my 2003 when I installed a manual M5R2 5-speed.
The PCM wants to "see" a neutral condition, so I hard-wired the leads on the transmission connector going into the PCM. The PCM now thinks that it is always in neutral. It will shift into 4L, but I get an "advance trac" error shortly after leaving the driveway in 2H. This may be related to not having the speedometer connected yet. Your tone wheel and pickup mount is the bomb! I am mounting a disc with a 6-hole pattern on the front of the rear driveshaft, then fabricating a mount for the sensor so that the axis of the sensor is parallel to the driveshaft and held away from the face of the disc about 0.030".
In the diagram below, you have the details of what goes on in the DTRS-- digital transmission range sensor of a 4R70W. Look at the DTRS box and imagine that the "needles" from the center post of each "PRND21" arc move together for each gear change. The default position for the diagram as it is shown is Park. So if you were to evaluate the connections that are made when in reverse, the pointer will move on all 7 connections. On the far left-hand arc, pin 9 will be connected to pin 11. On the second arc, pin 10 will be open, and so on.
In our case, we want the PCM to see a neutral condition all the time to go into 4L, since the former auto transmission must be in N and the brake pedal depressed. Of course I know that I need to be stopped to shift into 4L, but Ford could not count on every owner being that astute, so they had the PCM prevent the transfer case from shifting unless the auto trans was in N.
To communicate a Neutral condition to the PCM, pins 19, 17 and 20 on connector C175T were hard wired to pin 27 on the same connector C175T. C175T is the big connector that goes into the PCM. I put a couple of resistors in parallel that would get me 270 ohms between pin 17 and 20.
When I get my OSS sensor connected to the pulse wheel on the front of my driveshaft, I will put the signal across pins 27 and 25 as shown below.
For the clutch pedal, there are (on my switch anyway) a number of choices. I had some normally open and some normally closed switches. I found a set of pins that was normally open when the pedal is at rest and closed when all the way down. I connected this set of pins to pins 10 and 12 that came from the DTRS. This is so the start circuit will work with the intended safety funtion.
For reverse, I connected the switch on the transmission to pins 9 (LB/PK) and 11 (VT/Wh) which are wires that came from the former automatic on connector C167 (the one going into the DTRS). This turns on the reverse lights with the switch from the manual trans. My connector was missing from the transmission, but I got a new one from Rock Auto.
I got my wiring diagrams from a genuine Ford DVD service manual. I bought mine from a company called Taylor Automotive, which no longer sells them. You may have to go to the Motorcraft web site to buy one.
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If you need other diagram sections, just let me know and I can create pdf or jpg images.
Thanks for documenting your transmission swap here-- great work and nice write-up.
CR
My buddy's Bronco should be Parked out front of them on Garfield. We should meet up sometime when I get back from Kosovo (next September) Try not to cringe too much when you see the shape its in, mechanically though its runnin like its new 
