Got a motor for the "Shelley"-the '66 sunroof Beetle.  According to the former owner, it ran well when pulled a few months ago.  Here's what I'm doing to it while it's out (and it's not raining).
clean-clean-clean
adjust endplay (it's at .015)
replace all seals I can reasonably get to (including new pushrod tubes-I want to re-torque the heads anyway).
paint tin, heater boxes and exhaust

Anything important I'm leaving out?

Well, as long as it's out . . . like Herb said, check the compression.  I've got an old tranny you can use (provided you haul it off and KEEP it).  A compression check might turn up a problem that a visual inspection might miss.

Since you are going to pull the heads to replace the push rod tubes, you have a perfect oportunity to also visually check the condition of the cylinders.  If they don't show much wear, you might want to go ahead and hone them and replace the rings.  I know that lots of folks frown on re-ringing VW cylinders since new piston/cylinder sets are not all that expensive, but I've always had pretty good service out of re-ringing provided that the cylinders were in pretty decent shape to start with.

I'd also lap the valves, even if they look good and the compression check was ok.  While you have the valves out, give them a good visual inspection also.  If it's a dual port, check the heads very carefully.  Dual port heads love to crack when they get hot.  If you have cracks from the valves to the spark plug hole, I'd toss them . . . and consider going to single port.  If it's already a single port, I'd keep it that way . . . less top end, but better gas milage, better bottom end performance and MUCH more durable.

Another thing I always (well, almost always) do is put a little valve lapping compond on the top lip of an old cylinder and rock it around in the head to smooth out any imperfections on the mating surface.  Now, I don't really think that's a good idea on a high performance engine or when using all new parts, but with old used stock stuff it helps you get a good seal between the head and cylinder.

Since you're setting the end play, you have to replace the main seal, but don't forget to replace the O-ring in the flywheel while you have it off.

As long as the rear bearing is tight in the case and the engine can maintain good oil pressure when it's warm, you can get a lot of miles out of a minor top end rebuild . . . the engine that I had in Homer is a testiment to that.  I spent $40 on that rebuild.  Yes, it only lasted 15,000 miles, but it came apart only becaused I pushed it way past it's limit from about 1/2 of those miles . . . and even then, it wasn't the top end that failed.  That engine has a big hole in the top of the block, but it still has good compression on the 3 cylinders that are hooked to the crank.

No, the transmission doesn't work, at least as a transmission, but it would function nicely as a test stand.  You can just bolt the engine and a starter up to it, wire the starter to a battery, and spin the engine to do a compression check . . .  or run a hot wire to the coil and hook a gas line up to the fuel pump and drop the other end of the line in a gas can (keep the gas a long way from the engine though!!!) and fire it up on the ground.  Or, you can go all out.  I've got a friend who gutted an old tranny, welded up an angle iron frame with heavy duty casters, put a battery box, voltage regulator, idiot lights for the oil pressure and generator, an ignition switch, and a small gas tank with a cut off valve.  You can roll the engine on a floor jack into the stand, bolt it up and hook up the gas, coil, and generator just like you were installing it in a bug and fire the engine up and run it.  It's great for testing new engines for leaks and other problems . . . it sure beats getting the engine installed and finding out you have a leaking push rod tube seal!  Anyway, if you want a tranny for an engine test stand, come get one.  I know I have two, and I think I have three!

Yeah, honing is just running the rocks on a drill to break the glaze on the clyinders.  You want to leave a "crosshatch" pattern in the walls so the new rings will break in properly.

Lapping the valves is easy.  Take the springs off, and clean everything up really good.  Then put lapping compound (for lack of a better description, it's liquid sand paper) on the sealing surface of the valve and drop in back in place.  You stick a tool that is really nothing more than one of those suction cup darts from a kids dart gun on the valve head and rock the valve around so that it cleans up and smooths out any imperfections on the valve face or seat.  It's nowhere near as good as grinding the valves to the correct angles and resurfacing the seats, but much better than doing nothing.

The thing with the cylinder is basically the same as lapping the valves, only your cleaning up the surface between the cylinder and head.

Oh, and make sure you get all of the lapping compound cleaned up . . . like I said the stuff is like liquid sand paper and you sure don't want it in and engine that has no oil filter.

If you are looking for a single port manifold, I have one or two, but they might also be plugged.  I'll check and see.