First off, shout out to @tr3flip
for coming up with this method. He saved me a load of work.
TL;DR: If you remove the radiator, top half of the intake manifold, and the clutch, you'll have enough room to pull the transmission out through the top. The engine does not need to be supported, the mounts remain and hold it in place.
My basic method of lifting consisted of a shop crane (cherry picker), anchor shackle, and a ratchet strap. I hung the shackle (pin side up) from the hoist hook, and hooked the ratchet strap onto the front and rear lifting eyes. Using the ratchet strap as a sling through the shackle, I was able to easily rotate the transmission along it's output shaft axis to help with maneuvering it in place. I'm sure you could use chain, however the synthetic sling was low friction enough to be able to slide it through the anchor shackle to give me another degree of freedom with maneuvering.
Step 1: Remove all the normal stuff: axles, half shaft, shift cables, etc.
Step 2: Drain and remove the radiator
Step 3: Remove the upper portion of the intake manifold. You should now have enough room to maneuver.
Step 4: Unbolt the transmission, pull toward the driver's side wheel and tilt away to access the clutch bolts. Note: one of the rear mount bolts won't be able to come out after you unbolt it. This is fine, just let it slide back and stay in place. You do not have to remove the starter, however you will need to remove the lower bolt, which bolts into the transmission case.
Step 5: Rotate the clutch / flywheel and unbolt the clutch assembly.
Step 6: With the clutch out, you should be able to maneuver the transmission up and out. I recommend unbolting the fuse box and strapping it to the side to keep it out of the way.
Step 7: Change the flywheel and / or the rear main seal while the transmission is out.
Step 8: With your new pilot bushing and high temp urea greased transmission, you're ready to reinstall
Step 9: Lower (new) transmission back into the car, and maneuver with the gearbox portion back toward the wheel. Set the pressure plate into the transmission clutch housing around the output shaft. Using the alignment tool, set the new clutch disc on the the flywheel (you may be able to wiggle around without doing this, I just found this easier). Slide the pressure plate over and on top of the clutch disc, and install all the bolts. You will need to rotate back and forth to reach them all.
Step 10: With the pressure plate torqued down, remove the alignment tool and slide the transmission over and stab the spindle.
Step 11: Put all the little bits back together!
Let me know if you have questions. This is pretty general, but feel free to ask specific details.