I'm not sure if these have been mentioned before, but a couple thoughts/ideas;
1) use one pickup. That bass, and a lot of PJ's, have enough distance AND tonal variation between pickups that they can interact oddly
2) Don't use a middle pickup volume. 100% on the P, 0 on the J
3) Start with flat EQ on the DI and listen for the phasey bit. Add EQ judiciously, cutting more than boosting at first if you can
It's not a bad sound to start with, so it's not a big worry. OTOH, every little bit contributes.