Rusty-Bug-Man,
Just looking through your adventures. Looks like a lot of progress but a lot of labor on just about every system or body part. That's some commitment

I noticed on #640 that you wondered if the boot goes in the cross member hole. It is, as you installed, a press fit seal.
You have a lot of the car together already but I would have recommended you replace or add a 1/4" SS fuel line in the tunnel. If you, or next owner, ever decide to build a high horsepower motor, the stock line might be a restriction. It is easiest to replace when the body is off. Did you cut open the tunnel to reweld the clutch cable tube. There may be fractures or rust after all these years. If rusted, you may have to replace it.
Additionally I would advise you use urethane rear transmission mounts. Urethane front mount would be good but probably not needed. I have seen a lot of VWs with oil getting on the stock rubber mounts, as yours did, and they will deteriorate over time. If you use urethane mounts they are a bit stronger and you won't have to replace them again (cheap insurance).
Make sure you paint the brake line heading for the rear along the tunnel if it is not SS. Water can collect by the tunnel,during rainy seasons, and eventually rust it out.
Also I would recommend putting a 3/4" sway bar on the rear of the car since it has a swing axle. Also install caster shims on the lower front axle tube (very easy/cheap to make from pipe stock). Handling will be greatly improved, especially at highway speeds.
In #779, if the pulley moves in/out, I would suspect you have not put the flywheel on and/or have not set the end play yet. The front main bearing has a surface for shims to run on between it and the flywheel. After you set the end play (probably about .004" to .005"), you should not be able to see the pulley move in/out. Once that is done, check the pulley to see if it is bent. Bends generally mean someone has pried on the pulley with pry bars or screwdrivers to remove it.
Keep up the good work and us informed with your progress.