basically, 2 ways to do the swap... Pull the engine/trans together, or just drop the trans.
As per the ussual, my pref is to pull the engine/trans together and do whatever else you want to do to the engine while it's out. (pan gasket, main seals, bearings, oil pump, w/e else you can think of.) To do this, start by draining all the fluids (trans fluid, coolant, oil doesn't really need to be drained) Pull the radiator, D/C the boost hoses, oil and trans lines, take off all of the intake pipes, DC all of the plugs coming from the body harness to the engine near the alternator, D/C the fuel line, pull the + and - cables from the battery so they are loose and can remain connected to the starter and block (batt should be D/Cd before work is started, btw) remove wairing harness **see later**, jack the car up, take out the 4 drive shaft bolts, remove the 2 carrier bearing bolts from the body, pull out the driveshaft from the trans, D/C the shift linkage from the pass side of the trans as well as the speedo cable, put a jack under the trans, undo the 4 bolts, move back toward the front of the engine, take off the lower engine/trans brackets, remove inspection plate, take out the torque converter bolts (will be easier than doing it w/ the engine hanging on the cherry picker), undo the 2 engine mount bolts from the bottom of the engine (going up from the bottom), lower the car back down *watch the jack on the trans*, hook your chain to the engine, lift engine up until it 'pops' loose, then bring it up... forwards... up... forward... up.. for... you get it. The trick is to get to people and have one person stand on the trans to keep it from raping your firewall and to make them feel important. TADA!
**intake**
Some people feel like pulling the actual intake plenum off and DC'ing every freaking plug on the engine, but I have found it easier to take out the glove box and top cover inside it, take the 4 screws out of the ECU, unhook all of the clips coming from the engine harness, and just pulling it out through the firewall. Dont worry about not being able to get it back through, it's really easy w/ some needle nose pliers and a little bit of patience.
now to the 'swap'.
Take out the Auto brake pedal, 1 bolt and a pin I think, it's pretty obvious what you have to do. put the clutch pedal assy up into place (note front bolt hole is hiddin by the rubber cover thing under the dash) go back out to the engine bay, pop out the plugs for the clutch MC. shove it in the holes, tighten it up (two nuts inside the car... complete PITA, IMO, put a new one in when you do it $40 well spent) hook up the clutch pedal w/ the pin, adjust it out until it doesn't turn easily w/ your fingers.
Run clutch line down to the Slave area.
Take off starter and the rest of the trans bolts. pull apart engine/trans. take off flexplate. Replace rear main seal (you're already there...) install pilot bearing, put on newly resurfaced flywheel :icon_bigg put clutch disc on, noting flywheel side is on the right side, pressure plate/TOB, and torque to spec (14lbs or somethng weak like that) put r154 onto engine, tighten up, install throw out bearing fork, put starter back on, replace the engine/trans braces. Oh, and do whatever work you want to do while engine/trans are seperated. ***JUMP THE NEAUTRAL SAFETY SWITCH*** I did mine by cutting the old plug from the trans and tying the two correct wires together and putting it back onto the harness on the engine.
Remove auto shifter from car...
put it back in w/ the order reversed.
Instal clutch slave, bleed clutch system, put on the 5sp front half of the driveshaft... fill trans up w/ gear oil, reinstall speedo cable... reinstall radiator, add coolant, reconnect the oil cooler lines, put boost hoses back on, double check all your connections, and you should me pretty much there.
anything I missed, my bad.