OK, I know this isn't a tone Phil ever had, but I was messing around with the EQ settings on my rig, and found a bass tone that I call the best of both worlds between Phil's crunchy tone in the 90's and his current tone with Furthur. I really can't describe it better than that. I know it isn't the exact tone Phil has ever had, but it's just amazing. For the record, I don't use a pick, but I somehow managed to adjust the EQ enough so it sounds like Phil.
My rig is:
Eden Navigator preamp
Meyer CP-10 Parametric EQ
QSC PLX 1602 Poweramp
Bass: Some cheap Ibanez 6-string (I had a Modulus Q6 TBX but had to sell it due to debt )
Here's a picture of the EQ settings if any of you are interested. Sorry it's large and partially cut off, if you want to see the whole thing you can right click and press "view image".