Ricks sound pretty different from Fenders in the lows, and I haven't worked with them enough to have proven methods of coping. Ricks always seemed to have ample mids and top, but the bottom just isn't as there. Maybe you're overcompensating and that's causing the problems. If you want big bass, you might be better off with a Precison.
I believe SWR's were something of a standard in LA sessions for a while, so it should be workable. I'd offer that I've never had luck with a biamped bass rig, and I prefer to avoid cabs with a tweeter and crossover. Try to make sure the sound you want is coming out of the amp first, because its nearly impossible to fix after the fact.
What mic have you been using? If your getting to muddy a sound, try an omni to eliminate the proximity boost in low frequencies. Maybe the quicker transient response of a condensor mic is called for, in which case I'd offer that you might want to try small diaphragm models in addition to the usual suspect large diaphragm models people recomend.
If using the Mackie pres, avoid using the eq if at all possible (get the sound at the amp and with mic placement) and use the direct out to bypass the summing buses.
IME, the Mackie 1/4" inputs work for instrument level stuff, but sound pretty lousy for it. If you want to do DI, invest in a good direct box. The Countryman is a long running standard, and there are host of other good ones out there. Some mic pre's also have great DI inputs so if you're shopping for a pre and don't have a DI, consider that function in your search. I've even heard some people with no love for Behringer like the Ultra DI, at about $40 I think, though I can't personally attest to it being decent.
I haven't messed with multiband compression on bass and don't think it's typically used for it, and I imagine it could be part of the problem. Since you're going into digital, for less aggressive styles I'd suggest just a good soft knee limiter to tame peaks. Compression could be helpful for slapping, but it can sometimes be a bit much for more laid back playing.
Hope this helps some.
Bear