I know thread resurrection sue me. Always hated that burgundy cheromanche, it's just way out of proportion. As is the OP's
still an interesting build from the standpoint of what can go wrong that no one ever really suspects.
Jeepers tend to be can do jump in and start cutting types. But there's some obvious lessons here...
That rear window, and lower rear door, has to be figured out and even fabricated (even if only roughly) before you finish grafting the main bits together. you can't assume the back (latching) end of your door will line up and correctly mate with the door opening, because the B pilar on a XJ might not be pointing exactly square with the new "C pilar" (the MJ B pilar becomes the C pilar).
Two of the only really finished Cheromanche's both went the half way compromise rout, by either leaving the 4 door opening and using the 4 door rear doors (see below), or by using the 4dr door and grafting "filler panels" in (see the upper rear door of the burgundy cheromanche above)
A more professional compromise would be to use the 2 door (or MJ) door opening at the C pilar, and then graft the lower rear corner of a MJ or 2d XJ door, so you eliminate the wheel housing shape from the 4dr XJ C pilar. this allows you to use the 4rd window/door frame, while making it look less "hack" on the lower portion.
Everyone loves those blue photochop MJ's the only problem is the rear door and window are a tall order. you can do them with the above graft suggestion for the lower rear part of the door, and then have custom glass made to fit your custom frabricated upper rear door frame...
It would be much easier and in the end maybe better looking to just forgo the MJ rear window and use the metal rear hatch/graft of an 97+ XJ. This kills two birds:
A) your roof line problem becomes much easier (you're effectively shortening the rear of a 4dr XJ) so you take out ('section') a few feet of the cargo area, and graft the roof and upper D pilar of the 4 dr, and graft in the lower back of the MJ cab. plus the bed rails.
B) Fixes your upper door lines to look like they belong there. and your lower door lines can use the lower rear corner of an MJ style door.
C) Optionally you can get REAL fancy and do something Chevy Avalanche-like with the rear hatch.
This is my personal preference, and what I plan to do eventually myself (retirement project maybe?)
My personal idea is to use the upper half of the metal 97+ hatch cut off the bottom, use the D pilar of that 4dr XJ, and the lower back cab of the MJ. In such a way as I end up with a mini-hatch and possibly a fold down lower hatch, with a bobbed MJ bed.
Slightly longer than this, with slightly longer wheelbase (not a photochop, should be familiar to
old timers):
In short something very Explorer Sport-trac or 4 door Durago proportioned.