By getting rid of the auto you'll eliminate all your transmission lines and such. Outside of the you'll need the bell housing, flywheel, shifter, clutch kit, and clutch fork. Oh yea, you'll need the clutch cable that goes through the firewall, but basically you're swapping a system with a lot of parts to a much simpler system. And I think there's only one electrical wire going to a T-5, a ground of some sort. If you're going used though I would highly recommend replacing the clutch fork pivot stud and the throwout bearing retainer assembly. Those tend to get worn with time and the smoothness of new ones is very worth it.
This is a pretty decent list. I've done it before. For a 99-04 car, I'd reccommend trying to find a 99-04 trans, as the 94-98 ones didn't have the electronic speedo pickup, so I'm not sure what you would do about the speedo. They had a gear driven one.
Otherwise his list is pretty complete, You need
- bell housing and bolts ( I think you can reuse the auto bolts)
-flywheel for a manual
-flywheel bolts (flexplate bolts are shorter and won't work)
- different driveshaft (I just swapped the yoke... the yoke on the transmission side is different between auto/manual - rear end size is the same)
-Shifter (get an aftermarket short throw IMO)
- clutch cable, clutch quadrant - I'd recommend going aftermarket and getting a firewall adjuster/clutch quadrant from UPR/MM/ the likes. Get an OE ford cable though.
- shifter bezel/lower shifter boot
- pilot bearing and throwout bearing - get ford OEM - the aftermarket throw out bearings suck
- pedal assembly (you already have this you said).
- you have to cut out the sheet metal where the shifter goes a slight bit
- You can make due with the automatic wiring harness, you just have to jump two wires together in it to override the neutral safety switch - the car won't start if you don't do this using the auto trans harness - I don't remember the wires off the top of my head. Just be careful as the car will start without a clutch, and your cruise control may or may not work.
You will also have to find the wires for the reverse lights and splice the reverse light connector for a t5 on (you can buy them cheap from LMR and the like I believe).
I eventually changed over to the manual harness, as it cleans up underneath the car (the auto will have some random connectors you don't use anymore) and the rear o2 sensor plugs are positioned differently. It took me a long time to find a harness though.
That should be about it... as far as the computer - you have two options -
1. Switch over to a manual ECU - Plug and play, just find one from 99-00 or 01-04, as the 99-00 ECU probably can't control the IMRC butterflys if you have a 01-04. Not 100% on that. You will have to take the car to ford to mes with the PATS system to swap ECU's.
2. Get a tuner. With the SCT software you (well, a tuner with the pro software) can turn off all the automatic stuff in a tune, and the car will function fine. I am still to this day running the original automatic ECU.
With a manual, you will lose some weight off the car (the auto is HEAVY) and be able to bang gears yourself. I don't regret the swap at all.
---------- Post added at 10:06 PM ---------- Previous post was at 10:03 PM ----------
Also, I forgot - the transmission cross brace/mount thingy - is the same between auto and manual. You can re-use your old one. I had a "swap kit" so I had another one, I actually couldn't get the one on my auto trans off. lol