Another small update. While I got the transmission, the shifter I did not have. The stub that came with the transmission has the retaining flat on the driver's side and the guide pin slot the front when looking from the behind the bellhousing. In my B3000 the flat is on the passenger side. This means I can't easily swap my M5R1 shifter to the new M5R2 transmission. It also turns out that gear shifter levers for F150s are unobtainium. The salvage guys don't keep them, junkyards don't hold onto them and no one appears to sell them on eBay. However, I found a local company called ManTrans that happened to have a correct fitting shifter lever in their junkpile. $50 dollars later I have the shifter lever, the boot and the retaining bolt. It does fit correctly and I can now move the M5R2 through all the gears. Daryl, the owner of ManTrans was kind enough to say that if I pulled the shifter plate and sent him a video of the gears moving he would let me know if I needed to do any servicing before installing the transmission.
For those who don't know, the M5R2 does have some of the same quirks as it's smaller sibling the M5R1. Both use Dex/Merc ATF for fluid. Both have an issue of the shift rail plugs leaking and causing premature failure(These plugs are located on the shifter plate, behind where the shifter lever is located.) The default plugs are rubber but Dorman makes a small metal freeze plug that fits perfectly resolves that particular issue. Both can wind up with very sloppy shifting due to the shifter bushing and pins wearing out. That can be fixed with a repair kit from Dorman.
The last thing I need to complete the transmission stack as it were is a knob for the shifter. The shifter knobs for these trans is a splined fit versus screw on so it limits what shifter knobs you can use. It turns out the stock shifter knob used in the B Series is again unobtainium. I can find the shifter knob for the later model Rangers without issue but I don't like the look. Either I'll have to settle for that or wait until the actual swap then transfer over the shift knob being used for my M5R1 presently in service.