I spent a lot of time years ago trying to figure this out exactly, but there is a lot of conflicting information out there. Flea has always been a big "plug in and play" kind of guy in the studio, and so if you look at what equipment he was playing around that time, it's likely that was the gear that was involved. Knowing how the producer (Brendan O'Brien) operates in the studio, he will sometimes record 3 bass tracks or more: a DI, a cleaner amp, and a distorted amp. With those options, the more aggressive songs were probably mixed with the more aggressive sounding amp turned up, etc. I've seen parts of the "Funky Monks" video where I can see an 800RB in the shot, but I don't see any bass cabs in the room with it. Also, to my ear, there is definitely a few songs at least that were recorded with an SVT 8x10, as that cab has a very characteristic sound. Take a listen to the bass master track of Mellowship Slinky, that sounds very much like an Ampeg 8x10 to me.
What it boils down to, is that it's probably a combo of a DI, GK, Ampeg, and Mesa. Even though he used the Wal on most songs, some songs are the front pickup only, some songs have both pickups but no filter engaged, and some are at least one of the filters engaged. It's all over the map really!
One other comment I will make is that you can actually another master track of Flea's Wal by googling / Youtubing the bass master track for "You Oughta Know" by Alanis Morissette. When you hear that, you can get an understanding of how much the studio can alter the core sound of an instrument, cause Flea's Wal definitely has the typical thick / "darkish" tone that all of my Wals have had. To me that track sounds like it was recorded with an Ampeg B15.
ANYWAY. More things to check out for you if you have a few minutes to kill!