This is a seven page thread, and we've had only four or five entries from the OP, Destructobot. Maybe we scared him away, but we need to hear an update.
Also, everyone should go back and reread his posts. He specifically stated his guitar player doesn't always use the Marshall stack, he doesn't always crank it, and he often uses a power attenuator. He (the guitar player) also uses a Marshall 50 watt or a Fender Quad Reverb.
Destructobot also said that the quad with fuzz and turned up to 3 drowned his bass out. I believe he said something about playing his bass through the Marshall too (for comparison). It also seems that he is using sensible eq settings.
OP says he has done the battery phase test. Hasn't replied about his speaker cords, amp placement, other venues or his perception of how loud the rest of the band is.
Maybe the band IS way too loud. Maybe there is something wrong with one or more of the components in his signal chain. It IS possible to replace a bad cord with a brand new cord, only to discover that the new cord is also bad. It happens.
So anyway, a lot of the advice here is well intended, sensible and possibly helpful. But we are getting a little carried away with our assumptions about what his problem is. As I said erlier in my post, go back and reread how many things he HASN'T said that we are now incorporating into OUR interpretation of his post.