I did the m6 swap on my auto car and most of pics did get deleted but I figured I'd try to do a comprehensive writeup and use pica from other sources, if anyone doesnt want their pics up just send me a pm....
Parts list....
Fbody/GTO T56 (gto t56 will need fbody shifter lever, shifter, and ls2 starter)
T56 crossmember
T56/T5 torque arm mount
T56/T5 manual pedals
T56 center console.
Clutch M/C with reservoir
Slave
Clutch assembly
Flywheel and clutch bolts
Lower rubber floor boot for 6 speed
I like to get the interior done first. So go into the car and unbolt the console. There are 2 10mm bolts under the armrest and 2 more in the very front of the console closest to the pedals. There are also 2 small 7mm screws that hold in the top shifter plate. Remove the small u-clip on the back of the shifter knob and pull it off.
Attachment 24458
You will now be looking at the auto shifter assembly... Unbolt the 10mm bolts that hold it in, unplug the small electrical harness on the side and disregard for now. The large pulg near the shifter will be used so dont destroy that. Next unhook the shifter cable and push it through the grommet underneathe the car. you will now be looking at this...
Attachment 24459
As you can see there are 6 rivet holes you will need to drill out and you will need to cut the autobrace from the back console brace as shown in the pic. Once this is all done you are now ready to cut the hole for the shifter. There are honestly no measurements for this I just did it by eye and the pics and just had to trim a little bit when I got the tranny in.
Attachment 24460
Once this is done you are now ready top swap the pedals and drill the hole for the M/C. First thing is to take off all the plastic covers on the pedals they are just held on with some small clips and screws. Once these are off you can now loosen the pedals, first unplug the brake and cruise switches and unscrew them out of their sockets. Next remove the 6 (i think) 13mm bolts on the pedals and rotate them in a counter clockwise motion over the steering column to remove, there is no easy way to do this it just takes finese lol. Install the new manual pedals in reverse order and reinstall the switches and bolts. you will now notice you have a perfect template for the mc hole....
Attachment 24461
The center of the hole should be drilled 4 1/4" from the steering shaft and the top of the hole should be level with the top steering bolt. The hbole saw needed here is 1 3/4. Of you notice here in the pic there is a stud that was used to hold the shift lock cable in the auto. it is fine with the stock master but if you choose to use a Tick m/c it needs to be removed. The m6 cars have a small plate tack welded the the firewall here where the mc goes for added support. MAKE SURE TO ADD A PLATE. If you just mount the mc to the a4 firewall it will flex and may cause issues bleeding and eventually crack the firewall. I simply made a brace plate out of 1/8" alum. next bolt up the m/c and reservoir of your choice.
Ok, no beer breaks yet. Jack up the car as humanly possible and crawl underneath. Make sure the batt is disconnected and remove the starter. Now by turning the crankshaft find the 3 torque converter bolts on the flywheel and remove them. You are now ready to begin removing the 4l60e. Remove the bolts holding in the torque arm mount and driveshaft and transmission crossmember. With a jack supporting the transmission lower it so you can see the belhousing bolts and wire harness. Unplug the big wiring harness VSS and o2 connectors and set aside. Now get about 3ft of extensions and from behind the tranny remove the top bellhousing bolts working your way towards the bottom.
Once you're done here have a buddy hold the jack under the oil pan and both of you wiggle the tranny free with some effort it should come off. New move the flexplate bolts with an impact. YOU ARE NOW DONE DISASSEMBLING CRAP lol.
Get your new clutch assembly and pilot bearing... Tap it in with a socket or install tool and install the clutch and flywheel using the correct bolts. Next bolt the t56 bellhousing in place using the old bolts.
Attachment 24462
install your NEW GM style slave onto the transmission and move it under the car. Now the t56 frankly sucks to lift because its not flat so however you want to get it up there go ahead lol once its bolted to the bellhousing proceed to the next step.
Now that the tranny is bolted to the engine install the trans crossmember and reuse your auto trans mount. Also reinstall the torque arm using the new t56 mount. Bolt back up the driveshaft, exhaustand connect the master line to the slave routed out of the way of the exhaust. Now its time to get back into the car to finish things up.
Now that your back inside its time to do some wiring. Take the large plug that went into the auto shifter and cut the head completely off. Now the way to wire it is like this....This is not mine lol my connections were all heat shrunk and crimped lol. Before i continue I highly recommend going on ebay and ordering the pigtails connectors for the t56 reverse lights, and reverse lockout to make this all easier.
Attachment 24463
Connect the orange and black wires together to make the hatch release function. The green and brown wires go underneath the car to the reverse light socket on the t56 the polarity here does not matter. Next look at the green and purple wires these go to the switch on the clutch pedal to allow the car to start they are polarity sensitive so if you do not have the color coded harness on the pedal and have to make your own just try it both ways to see what works. Now your vss harness under the car may reach the t56 sensor but if no just extend it about 8-10" to reach i had to do this with mine. The hardest bit of wiring here is this and its not even that bad lol.
The reverse lockout solenoid allows you to enter reverse when the car is going below 3mph. Without it you will have to muscle and over power the solenoid to get into reverse. The way the pcm does this is by sending a constant 12v signal to the solenoid located on the shifter base and then momentarily grounds the solenoid when speed is <3 mph we need to replicate this to make it function correctly.
NOTE:wire color on pcm is for 99-02 cars only 98 is different.
Go under the car and find the auto harness plug now located the tan wire in the plug and cut it thjis is the TCC lockup wire which wont be used with the manual. Run a wire from the ground side of the reverse lockout solenoid to this wire. Now go up to the pcm and go to the red connector. Now remove the tan wire that is in pin 42 of the red connector and move it over to pin 44 which controls the reverse lockout feature. I'm not going into detail on how to repin things but youtube shows you how and the job should take only 10 mins... Now find a keyed 12v to supply the reverse lockout with power I simply tapped into the accessory charger on the lower console. WIRING IS DONE. Tape and ziptie all the other wires out of the way.
Attachment 24464
Install the shifter of your choice along with the rubber lower shift boot with self tapping screws and then reassemble the console just as you pulled it apart but with the new m6 shift plate and leather top boot. Next bleed the clutch and re assemble your interior panels and go drive your new m6 converted car! You will need the tune flashed to an m6 one to make the reverse lockout work as well as turnoff a bunch of ses lights and asr light if you have TCS.
