The Modulus sound changed tour by tour and night by night IMHO. For me I get closest to the late 80's sound with an SWR-based rig, but the biggest factor by far are soapbar pickups, modern electronics, and the right pick. http://www.ebay.com/itm/TELEFUNKEN-Grap ... 1295wt_959
(huge thanks to Zambiland for giving me one of these!)
This pick is a little odd to use at first but it gets the absolute perfect attack, and that's really the key IMHO. He used so many basses and changed up his rig but always sounded like Phil, to me as long as you have the pick, any clean bass rig will do and Barts work just fine. I'm not sure which year he switched to EMG, 1991 would be my guess, after the Ken Smith tour. I'm using Barts and an ACG preamp in my 80's/90's Phil bass and getting a killer tone.
Here's the most recent example, and a good one because I had the ACG set about as "flat" as it goes with a little high treble boost. Rig is a GT Tubes pre (identical to Phil's from the late 80's to '95 or so, an SWR design) with the EQ set flat with the Aural Enhance knob at about 40%, into a Crown XLS2500 power amp and an Eden 1x15" and SWR Goliath Jr II 2x10".
(note, I played my Starfire for a few songs and a modded Fender/Warmoth precision for a couple, too. You'll hear which bass is which if you skip around)http://www.mediafire.com/?qfij74t0l41gap9http://www.mediafire.com/?nigsgdda16knina
Reading your post a little more carefully... I dont' see why you'd be lacking punch or clarity with that rig. If it were me, the first thing I'd do is stop all that EQing and start flat. I don't belive in "dialing in" a tone on a bass rig, it should sound good in most rooms with everything set flat, with the EQ knobs just there to correct for rooms that are unusually boomy or muffly or resonant at one frequency. If you don't like it when it's set at it's neutral setting, it's the wrong amp IMHO.