1. Am I correct in understanding that in actual vanilla/classic without these bugs you should keep JotC, and SoR up?
Yes
I'm assuming BoW for long boss fights? I'm also guessing that you never judge, because then you'd have to reapply JotC, and SoR, but correct me if I'm wrong.
You should have all relevant blessings in a raid setting. As for judging, you will judge Righteousness on cooldown. You will have to reapply your seal, but since Righteousness doesn't leave a debuff behind Crusader stays on the target to be refreshed by Melee swings.
2. So then what is the formula for determining how weapon speed/damage/DPS affects SoR bonus holy damage? The tooltip only says "slower weapons cause more holy damage per swing."
More or less, the speed of your weapon will not influence how much DPS Righteousness does by itself a meaningful amount. If your 1.0 weapon does 10 damage per swing, your 2.0 will do 20, your 3.0 30. That's not exact, but that's the method.
The build gets its teeth from abusing procs. SoR does the same damage on a fast weapon, but set percent buffs proc a lot more with a fast weapon and SoR doubling that chance.
Does both the weapon swing, AND the SoR holy damage give an opportunity for Thunderfury and maelstrom to proc?
Iirc, yes. That's the gist of this build.