Sorry for this ancient reply but IT WORKED!
Now no Phat II EQ or FAALTU(useless) as I liked to call it in my signal circuit. Simple J-bass configuration(vol-vol-tone) and it sounds way better than what it used to.
As far as the excess gain problem is concerned, its still there(probably a hint louder, I think). Still overdrives the amp but without the excessive lows which were present with the Phat II EQ. So, it is easier to fiddle around with the gain and master volume of the amp to get a cleaner tone while retaining the 'sound'.
The mod was as simple as 'stimulating' myself, it came naturally(no pun intended).
The first solution would simply be to find the input and output wire on the Phat II EQ, desolder them from EQ and solder them together. That way you'll permanently bypass it, and you can remove the battery and ignore that top knob altogether.
Followed this easy suggestion by Stealth and did the same with the earth wires. Also, I removed the pot altogether and kept it safely for another experiment(this one guy I've been chatting up via email about the same thing says Phat II EQ works well with a few Washburn basses).
Sound samples are on their way, wait just a lil while longer...