After you waste a couple weeks cutting a rewilding the flanges to be correct, and surfacing them within 0.005" of true, you can get back to work. I bolted them on with some copper RTV between the flange and Felpro gaskets. I used the stage 8 locking header bolts and tightened accordingly. All the threads were chased and lubed to prevent any crossthreading.
The balancer goes on like anything else. Dab of grey RTV in the keyway and pull it on with an installer, NOT THE BOLT. Learned that the hard way before.
Once you get it off the stand you can get to the backside. Pound in the one oil galley plug (with a little RTV if you're paranoid as fuck.)
Put a bead of grey RTV around the edge and install the rear cover. Let it sit a couple hours to set up and torque to spec. Install the oil seal. I cut a piece of PVC to size to drive it in square. I also put the dust cover in.
I then replaced the pilot bearing. I packed the cavity with soap and pushed it out with a dowel. Much easier to clean than grease. Drive the new one in flush with a block.
IMPORTANT: Put the spacer plate on before the flywheel.
Then put the flywheel on. Orient it correctly, thread in the bolts with a touch of Loctite, and torque to spec. Put your friction disc in with the alignment tool, followed by the pressure plate. Buy new clutch bolts because you're an idiot and forgot where the fuck yours went because your piece of shit has been sitting idle for so long. Slowly draw the pressure plate in, ensuring it stays square and the fingers stay flat, skipping around and only going a turn or two at a time. When it bottoms out, torque to spec.
Once that's done, put the transmission on. Inspect the clutch fork, TOB, and pivot stud. Mine had less than 500mi on them so they were good to go. Install the transmission, wiggling that stupid thing like hell to get it to seat FULLY. Don't draw it on with bolts. Get it flush against the block before you put the bolts in and torqued to spec.
BAM. Ready to throw in a car. Adding other accessories is optional and depends on your car and configuration.
You should have something like this:
Hopefully your engine doesn't grenade when you start it.