Here I am checking this thread yearssss later trying to find information on wiring my speedo. I successfully swapped my 99 gs to a 5 speed. It was a learning process and great to know I got it done, but it just wasn't worth the time, money and problems. Complete parts list:
Needed:
manual transmission (make sure it has the throw out arm)$500
clutch (should come with throwout bearing)$200
manual transmission rear tranny mount $50
slave cylinder $20
clutch line $10
master cylinder and reservoir $20
pedal assembly (with clutch pedal) $30
shifter (mount plate and cables) $15
shift boot $5
Optional:
5 speed ecu (raises redline 700 rpms) $200
5 speed radiator (thinner, gives more room) $150
5 speed cluster or new guage faces (shows appropriate redline) $50/$20
5 speed drive axles ($100 a piece)

Your best option is to buy a donor car and rape all the pieces youll need from it. Thats how I got the ecu, radiator and shift boot/guages. The mount plate for the shifter cables bolts right up, its a bitch getting them through the firewall, but just take out the tcu under the radio. The tcu is the transmission control unit, only used for the automatic transmission, so you dont need it. It has two bolts hold it to a mount plate, then slide it out the passenger side and unbolt the wiring harness from the bottom of it. That will give you more room to run the cables.

Theres prepunched holes under the driver side dash for the master cylinder, so just dremel them out or punch them out. Everyone says the pedal assembly was the hardest part but it wasn't for me.
When I was finished with the swap at first, my check engine light was on. When I swapped ecu's, it went off.

When you go to bolt the transmission to the engine, make sure your throwout bearing is installed properly. It has two little very very delicate fingers on the back side that hold it to the throw out arm. DO NOT break those fingers and make sure you slide the throwout bearing correctly onto the throwout arm. I broke one of the fingers and figured "f*ck it" but after I got the transmission assembly in and started the car up, the throwout bearing rattles around like a mofo in there. IT sounds really bad. When I roll up to stop lights, I push the clutch in a little bit to shut it up. So dont learn the hard way like myself.

As for wiring, I found a plug for the reverse sensor on the transmission which is on the driverside front of the transmission, its a round plug with two leads in it. I spliced the red/blue and black/white wires from the auto harness into a piggy tail plug for the reverse sensor.

For the starter problem, I spliced the black/yellow wire from the wiring harness into the ground for the reverse light (red/blue). This just grounds that wire, which would happen before when I had my car in park or neutral, allowing me to start my engine.
There's also a clutch safety switch right above where the clutch pedal bolts up, which I plugged my clutch into, but it doesnt work for me. You could run the black/yellow wire up to that switch and ground the other wire coming out of it, or just not be a moron and start your car in gear.

I also bought new drive axles for the conversion, but I couldve used my old ones. I broke a boot when I was taking one out, so I just bought both new ones.

The only problem I'm having now is the wiring for the speedometer. If anyone has any clue, please email me. I bought a piggytail plug for the speedo sensor and spliced the three wires into the matching wire colors from the ECU (on the bottom plug). The tcu is removed. Still no speedo.

I hope this helped anyone out whos thinking of doing a swap. It was a learning process and a pain in my ass but I got it all done in just a couple days, with much persistance. Buy everything you need before you start. I did it without a cherry picker. I just jacked the shit out of the car and put 4 jack stands along the sides to hold it up, then used a motorcycle jack to lower the engine/transmission assembly. Good luck!