Great that you found a case that could fit with just a little modding! FWIW I found a fabric store that sells "fur" similar to what is in a guitar case. I bought a couple of square meters of it that I have been using to cover either places where my cuts have left the foam exposed, or to cover foam pieces that I have cut to improve the fit of the guitar in the case.

It occurs to me that if get tired of unscrewing the spikes, you might be able to use steel slugs/dowels and rare earth magnets so that you can do a "quick release" for the spikes when you want to put it in the case. Something similar to what DeWalt and other tool makers use for quick release screwdriver and drill bits.

I have a set of Geezer Butler P-J bass pickups, BTW. They are awesome! One of the best bass pickups I have heard IMHO.

Do you already have the DP146? If not, it might be worth it to get another Geezer Butler P pickup. The DP 146 is about the same price as a Geezer Butler P. You'd be able to use JBass wiring harness. The quick connect for the J pickup is the same as for the P pickup, and they would likely relatively well balanced. The EMG is a sort of classic, alnico V bass pickup, where as the Dimarzio is a very hot modern ceramic pickup. That may be great, since they will be quite different from each other, and you can always turn the DM down with an independent volume control. That said, one of the things I like about my Geezer Butler set is that the P and J are pretty well balanced.

The other advantage, assuming that you have been bitten by the guitar building bug, is that you'd have your P+P bass for this project, and you'd have a J bass pickup and quick-connect harness for the next project. That EMG J is not an ordinary J pickup. EMG designed it to work with the P bass pickup. It's also alnico V, but it's also higher output and humbucking. It would sound pretty good on its own, or you could use the wiring harness with any of EMG's other passive bass pickups. They are also in about the same price range as the Billy Sheehans