Jr. ,
I'm not sure if my 96 is different than your 00 set up seeing that you have hyd assisted brakes. I'd take both pumps off as an assy and separate them on the bench. I removed one hose from the box and the other hose from the pump (where they screw into the mating parts). Again, yours might be different. If you just take the vac pump out, aligning the shafts without nicking the seal will be more difficult - not impossible, but more difficult.