Its a clutch swap with pedals pretty much. Then you move the speedo cable over for the clutch cable to go in. I did it back in 2000 on my old notch and it went fine. You can pull the steering column and that may make your pedal swap easier. They are easy to install, but sometimes reaching the bolts in such a tight area can be tough.
Its up to you if you wire in the VSS sensor. Either you want to start it w/o pushing the clutch in or you don't. You may want to make sure you have the right speedo gear for whatever gears you have too.
Pedals were the toughest part for me. I had my dash out at the same time, so i found it easier to feed the pedals in from the top.
Wiring up the NSS is easy. There are two plugs on the far left of the firewall you plug into the clutch pedal.
The one on the trans you do not need to do if you keep the AOD computer. That one is only used to tell the comp the trans is in nuetral and it's okay to dump codes. The AOD comp has this turned off. You actually want to run the AOD comp anyway. There are slight pinning differences between the 5-spd and AOD comp which may fry out the O2 harness.
In fact, swapping in a 5-spd EEC is a little more work because there are actually two harnesses that need to be changed - 02Harness and the Trans harness that runs into the car over to the driver's footpanel in order to make the NSS on the trans functional.
