I have the pypes shorties, and they don't tell you in the instructions that you will either need to jack the motor off the mounts, or use a ratcheting gear wrench and take the one bolt on each side off ONE-CLICK at a time. And put them back on ONE-CLICK at a time. The other 7 bolts per side are easy to get off with some PB Blaster, and the dipstick tube comes out easy as well. If you are going to do it I recommend doing mid-pipes too, because you have to take them off anyhow to do the install, may as well kill two birds with one stone.
From what I hear, you really pick up next to nothing with shorty headers. One of the guys near me said he couldn't feel a difference. Is there any particular reason you'd want shorties instead of long tubes?