So what was the condition of the gland nut? Was it torqued tight and correct, was it loose, did it explode? An over rev alone generally does not shear pins; a faulty, read cheep, or loose gland nut can with the over rev and a clutch dump.

I'm sure you can get the pins out one way or another. As long as the holes are not rounded then it can all be reinstalled and you might only have the over rev to deal with. Used push rods are cheep as they are generally the first thing to go in an over rev.

I'm just not rushing into a total tear down just yet but it is your decision.

More success, but what next.
I consulted with a trusted machinist, and without taking any of the engine apart, I was able to drill and tap the center of each of the pins with an 8-32 thread. The pins were apparently only case-hardened (a hard skin, but a softer core). I was then able to put a pair of vice-grips on the tap and draw out all 8 pins without any damage to the crank!
I now need to purchase new pins and begin reassembly.
DJD, to answer your questions, the gland nut has some damaged threads, and was backed-out of the crank at least a quarter inch. I'll need to buy a new one.
It sounds like I should remove and check the pushrods for straightness?
Should I replace the gland seal (especially now that it has chips in it from the drilling & tapping)? Can I just pry it out, it looks to be "glued" in with silicone stuff? Do I then push a new one in place and attach the flywheel with a new gland nut?

Now that I have things apart, I see the gland nut must have backed out of the crank. It rubbed against the clutch and kinda rubbed-over the area of the spline that inserts into the clutch. That's what's holding the clutch and input shaft together. They are still stuck. Even though I now have the engine apart from the tranny, the splined clutch is still stuck to the tranny input shaft. I've attached pics here of the nut and the clutch plate, perhaps you can see the damage.
Can I just replace the seal and the gland nut and bolt the clutch back to the flywheel thru the starter hole like I took it apart?

http://forums.pelicanparts.com/uploa...1271726078.jpg

http://forums.pelicanparts.com/uploa...1271726163.jpg

There's also misalignment of the black clutch plates on the steel part they are attached to. Are they supposed to be on center with each other? see photo showing 3/8" or so of the steel showing beyond one edge of the black clutch plate.

http://forums.pelicanparts.com/uploa...1271726349.jpg

Wow, what a trip but somewhat classic for a gland not that was not torqued correctly.

From here on out I would treat this like a total clutch job:

Remove the clutch disk from the shaft and splines.

Surface the flywheel

Replace the flywheel seal

Replace the soft iron gasket

Replace the gland nut

Check the end play

Replace the pins (obviously)

Replace the clutch disk and the plate

Replace the throughout bearing

You might as well do this right at this point as anything less will cause you problems later. Once it is back together, adjust the valves, fire it up and listen for bent push rods. They make a distinctive click - click when bent. They can be removed and checked for straight by rolling on a flat surface. Good used ones can be used as replacements.