First: Things you will need (for 03+ anyway)
5 Speed Transmission (3.55 or 3.94 etc)
Clutch, Flywheel, throwout bearing
Passenger side Axle from an MTX
Transmission upper mount and shift cable bracket
Transmission brace that runs from back of motor to above the passenger axle
Shift Cables with clips for both ends
MTX shifter (SRT or Standard Neon)
Booger Bushings for shift cables
MTX pedals with at least the bottom interlock switch (SRT or Standard Neon)
Hydraluic clutch setup (master cylinder to slave cylinder)
MTX PCM (preferably out of an 03 or 04)
About 10ft of wire (something like 14-16 gauge)
Haynes Manual (or other brand from a local auto store, you need it for torque specifications and such)
Way to haul the car to a dealership
Unless I'm forgetting something that should get you swapped to a 5 speed. I skipped over a lot of the little stuff like removing the console and I didn't specify everything needed to remove and install transmission. I mainly wanted to get a list of parts that are needed and share my knowledge of the wiring changes that are needed. So if you need a step by step for removing the transmission or shifter you probably don't need to be doing this swap by yourself, consult with a qualified mechanic or hire one to do it.
First off I swapped the pedals out. To me this was the hardest part cause your laying on your back. There's a good write up on how to do this if I can find it I'll post the link here. But I can't seem to find it. But for a heads up pull the brake booster out a good ways its makes things easier.
Also install the clutch master cylinder while the brake booster is pulled out. Tighten clutch master cylinder and pedals, hook the booster back up now.
Next I swapped the shifter. How to posted here viewtopic.php?t=43559. This was by far the easiest part. Also remove the key cylinder lock cable so the key can be removed. Loosen the shift cable square thing from the floor now. Install the MTX shifter.
Now onto the fun part. Jack the car up rather high. Enough to drop the transmission out the bottom. Remove wheels, hubs, axles. Remove airbox, battery and tray. Disconnect all connecters from the transmission. Undo the two ATX cooler lines coming off the front to the radiator. Remove throttle body and bellows tube, starter. Place a jack under the oil pan on the motor to support it while the transmission is out. Now you can take the torque converter bolts out and start loosening the bellhousing. Leave top two bolts in the bellhousing until you get the top transmission mount out (which is kind of a pain). Once you got that mount out you can remove the top two bellhousing bolts and drop the transmission out. The ATX is a heck of a lot heavier so have two people to do this job.
While the transmission is out drop the old shift cable out and install the MTX ones. Also swap the back bracket from the motor to the transmission right above the passenger axle. The ATX brace is to short (pictured below with green arrow).
Tape up the connectors for the ATX and secure them out of the way.
Swap the PCM to the MTX one. Install MTX flywheel and get the transmission ready to be set in (install throwout bearing, clutch, new axle seals, etc) Set the transmission back in the way the ATX came out. Start top two bellhousing bolts and install the top transmission mount. Tighten bellhousing and mounts. Now you can remove the jack from the oil pan on the motor. Rotate the flywheel to tighten the clutch to the flywheel. Transmission is now intact. Check all brackets and bellhousing. Install the slave cylinder and route the line to the master cylinder how you see fit. Install the starter and lower transmission brace (from oil pan to tranmission).
Hook up the shift cables with new bushings and install clips. Find the plug on the back of the motor by the exhaust that goes to nothing. It should be capped off. This is the speed sensor plug in for the 3 prong sensor on the back of the transmission. Plug it up to the speed sensor (pictured below circled in red)
Install the axles and hubs. Remember use the MTX passenger axle.
Thats the majority of the mechanical stuff. Now unto the wiring issues I ran into. You need to wire up the clutch interlock switch thats on the pedals (bottom one). One of the wires needs to be soldered in with the black wire on the brake pedal switch. Thats a ground. Now run a wire through the rubber plug in the firewall. Connect one end to the other wire on the clutch switch. Tie the wire up under the hood so it won't get nicked or cut. Pop the back off of 2nd connector (C3) from the top on the PCM it should be white on the computer side. Once you pop the back off you can see all the wires going in. You then need to slide the next section back which exposes the pins going into the connector. Its hard to explain and kind of tedious. I can get a picture of it soon. You also need to do this to the top connector (C4) which is the green pcm connector. Cut one the of wires on the top connector and pull a pin out. The top connector is the ATX stuff so none of the pins are needed there. Take that pin and insert it into slot/pin 21 (clutch interlock signal) on the 2nd connector (C3) from the top. Put the connectors back together and plug them into the PCM. Heres the page that shows the pins for the computers viewtopic.php?t=44196
Now for the speed sensor. There should be a plug or two plugs (depending on your car, this is where i ran into issues) up by the brake booster. Mine had two plugs but I know the 05 had one big one like pictured below.
Regardless, find that plug or plugs and cut the white with an orange tracer wire up by the connector. Solder a piece of wire to the end (the end going back to the motor) where you cut it. Route this piece of wire however you can where it will be out of the way. Run it down to the bottom black connector (C1) on the PCM. Pop the back cover off the bottom and the top PCM connector. Take a pin out of the top connector (C4) since its the ATX stuff and that connector is no longer used. Solder your new wire to that pin and place it in slot/pin 13 (speed sensor signal) on the bottom PCM connector (C1) cause there is no pin in hole 13. Put the plastic backs back on the connectors and plug them into the computer. Heres the page that shows the pins for the computers viewtopic.php?t=44196.
That will get you running and with a working speedometer and no engine codes. I'm still working on getting the reverse lights wired up, which is the little two prong sensor on the front of the transmission. I haven't sat down and looked through the wiring diagram for them but I will soon.
Now make sure everything is hooked back up and tight. Fill the transmission with fluid now with whatever you want. Theres different opinions here. Some use ATF-4 and other things. I use Mobil 1 High Mileage 10w-30. Install throttle body, battery. Install wheels and lower the car. First get in the car, make sure the shifter is in neutral, and turn the key and make sure the car won't turn over. Now depress the clutch and try and start the car. It should start for 3 seconds and cut off. If it does your golden. Now load the car and haul it to a dealership or someone with a computer who can flash your VIN and skim key into the MTX pcm. Just tell them you put in a used PCM and you need your VIN and Skim key code flashed to it. After that you should be rocking a 5 speed.
If you have questions just PM me and i'll see what i can do. Now go drive and feel the difference...
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) all 03+ for sale are abundant in this area but, seem to always pop up as autos. My question is if I were to go that route but say use the 03+ motor in the new car so I could build my 02 motor with some proper horse giving internal upgrades in the meantime. Could I run the NGC motor with my 02 tranny and PCM? From what I understand I would need to change a few sensors and use the 02 engine harness, and SKIM module and ignition cylinder/keys. Am I correct in all this? What I else am I missing. Obviously an 02 rolling chassis would be ideal but, cash cost and driving difference would be the biggest concerns there. Need opinions and advice. Please and thank you, guys. 
