This looks like a fun project, John! You'll have a very dependable, classic CJ when you finish, the V-6 is a winner. I have a good deal of information on the Buick V-6, both odd and even firing types, your nail head 225 plus the later 231 (3.8L) and 252. Buick took this design to the limit, and it was a G.M. mainstay powerplant for decades.
The Simple Green approach is new to me, although it sounds much healthier than a petroleum distillate/solvent parts washer—I know firsthand and can still identify the scent of the original Safety-Kleen solvent from a block away!
My aqueous-based parts washing cabinet can run industrial strength citrus derivative soaps. I'm currently using Goodson Tools' PJS-50 detergent and running the water/soap solution at about 145-150 degrees F for optimal results. A washing cabinet changed my work life dramatically, I've had the machine since the mid-'nineties, it's paid for itself ten times over. Your project reminds me of the CJ-5 I built for the Jeep CJ Rebuilder's Manual: 1946-71. I'd still be scraping down that frame, powertrain and axles if it hadn't been for this washing cabinet.
For those interested, my washer is a Walker (very well built though they are no longer in business) with a 2-hp/single phase 230V pump, two 4500W heating elements, a 1000 pound capacity turntable and 45 psi nozzles. The heated solution is approximately 53 gallons. Bought mine new, made sense at the time. If you stumble across a similar design, a used machine in good shape, consider buying it, especially if you do any volume of automotive work on older rolling stock like 4x4s!
Goodson also makes PD-50 and a PD-10 (small quantity) multipurpose degreaser (not for heated jet washing!). You'll like the cool automotive machine shop tools at the Goodson website, click on the image for a glimpse!
As for the Simple Green turning the gears and such black, that's likely the chemical reaction between the citrus concentrates, water and the impregnated, ancient gear oil chemistry...Shouldn't cause a big issue, all of the shafts, gears and such are case hardened and resistant to corrosion and etching.
The beauty of the nozzle/jet washing cabinet, preheated to 145-plus F before placing parts inside, is that critical components like iron castings will "flash dry" after washing by simply cracking open the cabinet door and waiting a few minutes before removing the pieces. No oxidation/rust issues...I need to demonstrate the Walker in a video, it's really a time saver...I'm very grateful!