Which way is the preferred way for case nut orientation ?
Q#1. Stamped numbers up or down ? Click to view attachment
Q#2. All on the same side of the case or alternating ?
Click to view attachment
Q#3a. These nuts originally came stock with what I assume was some pinkish rubber oil seal. Does anyone know what rubber gasket material can be substituted ?
Q#3b. Was the rubber gasket seal outside of nut or inside of nut towards the washer ?

Functionally: it doesn't matter.
I like to put all the numbers facing out/visible.

All on the same side in my opinion, but again, I don't think it matters functionally.

Possibly the earliest engines came with the sealed nuts, but most of the engines that I've disassembled which appeared to be original didn't have the sealed nuts. I've never used the sealed nuts on an engine and haven't had a problem. I wouldn't blame anyone for using them, but I would also never recommend them because they're unnecessary.

If you do use them, the sealing ring goes out. It's intended to seal the nut to the stud/bolt (thread sealing).

I used Loctite 565 sealant on both sides of both washers on every case bolt, but the case bolts are not one of the common leak areas, so you don't need to get crazy here. Just a light coat, just in case.