The main issue may be how well the JB Weld resists the abrasive blasting that usually precedes phosphating baths of any kind (Parker's or anyone else's). It may be severely eroded by that if it is exposed significantly.
I agree there is not likely to be chemical issue unless the bond is compromised. To avoid that, you want the epoxy applied to properly prepared, dead clean metal. Preferably, you want it on a matte surface. On small things I use one of the little Badger abrasive air brushes and aluminum oxide abrasive for this. It leaves a good matte surface. A similar surface is best for Parkerizing the rest of the metal, but it usually takes bigger blast equipment to prep the surface of a whole gun without getting an uneven surface.
You also want to follow good epoxy application practices. In general, on a non-absorbent surface, epoxy bonds are weak if they are too thin. I've seen some demos done where a shim or a small raised bump on the metal (automatic centerpunch applied to raise a little crater rim) was used to maintain at least a couple to five thousandths of film thickness to get good bond strength. So this is not a squeeze-together-with-clamps situation. You want the epoxy to have at least a little gap to fill. I suspect this has to do with getting the best cross-linking of epoxy resin molecules to occur, but don't actually know the details.
A hot lye bath is an industry standard practice for degreasing metal because it is inexpensive and easily rinsed off, but you need to know safe handling practices as it can burn skin badly. Chlorinated solvents work, if you can find any. I've actually had very good results just using Formula 409 degreasing cleaner and the Slip 2000 gun degreaser and cleaner. The main problem is the rinsing, which has to be very thorough. I've used a running hot tap water flush followed by boiling in distilled water to remove final traces and prevent mineral water spots from forming. When I remove a part from the boiling water, wearing disposable clean cotton gloves, I immediately shake any excess water free and let the residual heat flash dry the surface moisture off. This forms a micro thin blue oxide layer on the surface (visible only in the right incident light) that will protect it long enough to get your epoxy applied. If you need it to last longer, put the part into a sealed container like a pickle jar with a strong desiccant. IIRC, surface rust can't form in relative humidity lower than about 30% or so.
I've found Parkerizing (or other brand phosphating) to be easy to do in my home workshop. I have a stainless tank for the purpose that is large enough to hold rifle barrels, but I've done handgun parts in Pyrex cookware and even in cheap enamelware pots before. You can request a set of instructions from Brownells and read them to get some idea what's involved. They carry solutions made by the Parker company, and they tend to provide pretty good, thick deposits. Other brands are a little easier to work with and less costly and may be adequate.
Shooter's Solutions makes some. But get samples and try it out rather than start with your gun as the first Guinea pig. Shooter's Solutions also makes a hot bath degreaser.
