You can get the stock manifold out the top. It's kinda like pulling a round peg through a nearly large enough square hole though. You are getting it up past the EGR tube, the alternator, valve cover, map sensor etc etc etc. Out the bottom..it's a quick simple slide and out.
I find ratcheting wrenches are great, use them all the time. I also have a flex head longer handle ratchet and six point sockets. If you hold the right spots and make sure you aren't going off at odd angles, you won't round any nuts/bolt heads.
Planning ahead will save you a lot of time.. I bolt up the rear with a couple bolts, then mark the firewall where you need to move it. Pull header, move firewall, header back in. Taking the headers to a shop ahead of time and getting the bung in a different location would save install time. Also.. have some cold water on hand and don't mess around staring at things for hours. Remove nuts/bolts and set old parts to the side.. put new parts on and you'll be done faster than you think.
Have the torca clamps on hand. 2 x 2.25" and 2 x 3.00. Plan if you are going to cat it or not.
I pull the parts off. Plugs, move wires out of way, pull front/rear and undo from catback. Wipe the MLS stock gaskets and head straight to the rear and moving the firewall. Then it's clamp slid in place, crossover and front. Once you have them on the motor, you hop under and connect to the catback with new bolts you already grabbed.
That's the basic steps. If you don't screw around removing extra stuff and whining about angles or a scratch or two.. you'll be done pretty fast.