Great progress. Absolutely fantastic.
Two thoughts -
The starter issue is what has been bugging me. If I were you I would solve it this way - Through a custom bellhousing. This seems like a very expensive proposition but this is the method I have seen used with great success.
The flange that mounts to the engine is cut out of steel, about half inch thickness. You can have it CNCd or punch it out on a manual machine, your choice, but since the bellhousing appears to center on a ring on the engine, the actual alignment should be easy to gauge. On this flange, a new mounting location for the starter (probably on the driver's side below the transmission, hopefully it could tuck in beside the pan) is made. So, you have a plate that mounts to the engine, and a starter mount too.
Next step is to make another plate having the outer dimensions of the mounting flange of the bellhousing to transmission joint. Do not machine the bolt holes or the inner diameter at this point.
Both plates are then separated in order to replicate the overall length of the bellhousing through a rough jig. The centering and parallellism of the surfaces is mocked up but is not required to be perfect.
The outer surface of the bellhousing, joining both "flanges" is then fabricated by rolling some 1/4 plate into shape and welding. This is time consuming but is actually not that difficult with a large press and some homemade dies. Multiple pieces are used, welded together, and then ground, and what is left is a bellhousing - but the trans end is still unmachined.
The entire bellhousing is then chucked in a lathe using the bellhousing to engine centering ring as a reference point. The bellhousing to transmission case surface is faced on the lathe (or a rotary table on a mill), the center bore of the bellhousing to transmission flange is bored out, and you punch out the mounting bolts later (which are fairly non-critical if the center bores and centering rings are well machined).
This would allow you to hang your starter anywhere you like and would be an easily fabbed shop type project with comparable strength and accuracy to original equipment.
Second thought:
Am I correct in assuming that trans diag code reading is done through plugging in a diagnostic wire (connection) and then counting the flashes on the trans indicator light? I have very little transmission literature and am curious to find out if I need to acquire specialized diag equipment.