It would work, and sound great. I have that combo in an RGT220A, but the body on mine is Ash, it still sounds fantastic. Being that the LF/CL sound awesome in the standard EBMM JP6 w/ Basswood bodies, the JPM100 also has Basswood, so the tones would be the same, or very similar.
For what it's worth, keep in mind, if you do decide to do this, your JPM will no longer be a JPM, even if you decide to sell it. It's no longer stock, but modified. I'm not sure how collectors would appreciate a modified JPM with the pickups other than what came with the signature specs. If I were you, I'd leave them in there as the SS and AN are fantastic for that guitar. If you do swap them, keep the stock pups, either in the case or someplace for it to always be included or swapped back in the event you do ever decide to part ways with the guitar.
Now, you are like me, If I were to buy a JPM modded with newer JP pups, but had the stock ones to got with it, I'd buy it and leave them in there, like you plan to do.n