I have a B pipe in my FX1 so these suggestions are only from that experience and from the limited B, I have in my Blaster. I believe you are talking about cutting down the length of the hose from the stock chamber to the waterbox. For my FX1 I had to cut that hose. Factory pipe provided a template for that cut. If you go to Factory Pipe's site and look at the instrutions for 96+ SJ it looks like they now provide that elbow. Didn't know that. I am guessing that you could cut yours, but I don't have a template.
As for fitting the pipe. Try subtle rotations and repositioning of the chamber, then retighten the coupler clamps and the hose on the stinger end of the chamber. Try twisting that stinger hose also to reposition the pipe. Sometimes that is all it takes to get the chamber to stop rubbing on those spots. You may have to resort to making some very small dents in the chamber, but I think if you just play with it it will clear all of the obstructions. I'm sure someone with a SJ will post direct experience.
Good Luck bra!