The main gain of a front shackle reverse on a CJ-7, -5 or Scrambler (1976-up) is that the front axle "trails" from the frame, it does not anchor to the frame at the rear of the spring. You will notice a substantial gain when off-pavement and pushing against larger obstacles. Instead of the axle and springs driving all the force into the OEM frame anchors at the rear of the springs, the springs will be able to swing or pivot upward from your reverse anchor at the front (the "shackle reverse kit"). This allows the springs and axle to pivot easily instead of needing to compress the springs lengthwise before the springs and axle finally have no place to go but upward!
This is a very wise upgrade if installed properly, and it works better on the highway, too. The front axle trailing from spring anchors at the front allows it to track freely. The stock configuration had the frame pushing the front axle along from the rear/anchor ends of the springs.
A glaring example of trouble caused by the OEM spring configuration is the 1972-75 Jeep CJ. They did not have the frame integrity your later 1985 CJ has, and hard trail use would cause the frame to crack or break just rearward of the stock front spring anchors. This was caused by the severe force applied to the frame at that point when the vehicle pushed against obstacles. In part, it was also due to the poorly designed frame: The frame was boxed from the front bumper to just behind the spring anchors, then opened to a C-section. The failure was at the junction between the boxed section (anchors) and the open channel rail.
Note: Many CJs of this vintage have repaired/welded frames, we can discuss the best repair technique if anyone has this issue. I'd be pleased to handle this in the welding forum.
As a point of interest, the M38A1 military equivalent to the original CJ-5/6 has the front spring anchors at the front of the springs. My earlier Jeep CJ Rebuilder's Manual: 1946-71 features a 1955 CJ-5 that I restored and built up for the book. That earliest edition CJ-5 came with the M38A1 type spring configuration—a factory "shackle reverse" if you will! Can't explain why Jeep reverted to the MB/flat fender frame approach.
Big tires, littler lift is a trend now, and it does help with the center-of-gravity and roll center, for sure. The frame height for approach, departure and break over angles does not work as well as a chassis/suspension lift. If you have enough approach, departure and break over frame clearance for your purposes, the "body opening" can be a smart way to go! You will have the axle clearance "lift" of the big tires, especially 37" diameter.
Consider long-term planning around axle width for track increase. Like RareCJ8's Scrambler, a radical lift is offset by a wider track width, in his case it's the use of stock, full-size 3/4-ton truck axles. This wider track helps restore center-of-gravity from the dramatic chassis height increase. Wider track also helps with any degree of body lifting that can affect roll center and C.G.
If you plan to stuff 37" tires under that CJ, a wider track width may be a necessity for tire clearance and also can help restore vehicle stability. This goes back to your comments about the J-axle—would it be wise to maintain that full track width?
Could you configure spring perches for each side to center up that axle under your CJ-7? A D44 J-axle at the rear could be a match. Is the other end of that Wagoneer available? That 6-bolt wheel pattern is a common G.M. 1/2-ton 4x4 truck and full-size Jeep configuration, aftermarket wheels are still readily available...make sure the hub center fits!
On that subject, I unearthed a simpler fix for your 6-bolt to 5-bolt issue. Biggman100 brought Roadkill to our attention, and they have adapters for 6- to 5-bolt in your 5 on 5.5" configuration. Here's a link:
Adapters would also increase track width somewhat, without the need to use wider axle assemblies.