I don't think the Kitman guy, who is a retired dentist, has actually ever personally built a car. If I remember correctly (which is a big if), the man bought the remnants of what was, some time and several owners ago, Tom McBurnie's Thunder Ranch operation. TR indeed shipped rolling chassis with bodies mounted and doors and deck lids pre-hung. How they did it is probably not exactly a trade secret, but could be a bit of somewhat closely held trade knowledge.
No idea what McBurnie's up to these days or how to reach him. One of the follow-on companies was called Rock West Racing, and they seemed to have a relationship to Kitman, at least a few years ago. Maybe someone there can help.
One guy who almost certainly could knowledgeably advise here is Carey Hines of Beck/Special Edition, upon which whose earlier engineering the TR kit was based.
He's probably pretty busy building cars though, and it's not for me to tag him into this thread.
If it were my car I'd probably bodge it up terribly, but here's how I'd proceed:
First, level the chassis in the work space.
1. set the door in the space it's supposed to go, with no hardware on it. Use rubber blocks to shim it so the bottom gap is small but reasonable (I assume this is not a painted body and you'll be sanding those gaps later for final fitting before paint), check the top edge so it's right with the fender and rear quarter, and adjust with the shims until it's good.
2. Measure the outside front edge of the door and scribe two level lines on the outsides of the doors, across the front fender where the hinges should be centered. Extend it to the rear fender for later reference.
3. Same deal on the inside.
4. Remove the door and connect the lines on both the door mounting area and the inner thickness of the door.
5. Drop a plumb line down the center of that door mounting area, connecting the two level horizontal lines you just made. Then do the same on the door itself.
6. Now you have a grid with reference lines you can measure from. You have to figure out where, in that lateral space where the hinges fit, they need to be. For this I'd consult an old CMC build manual, and/or maybe get someone here with an old Beck or pan-based IM car to stick a tape measure in their door jambs.
This is tricky because you may or may not be using the same hinge as those other examples. My guess would be that you want the hinges placed as close to the outside of the door--the exterior of the car--as you can get away with while still hitting the steel that should be embedded in the fiberglass in the door and the door jamb.
Well, hell, this is all my guess!
Here's a tutorial on hanging doors on an old Mercury. Obviously we won't need a door dolly or to hang it crooked to account for the weight of the window regulator!
Good luck. Hope I haven't just wasted both our time.