Slow down there, pilgrim... one thing at a time. I'll try to take this in order.
The timing marks changed when the pumps changed. Either timing cover will physically work with either water pump, it's just that a mismatched setup will have the timing scale obscured by the pump inlet. It has nothing to do with the air conditioning, it's mounted up top, somewhat centered.
As far as the necessity of an AC dedicated water pump, look at what Mopar did. Only factory AC equipped cars got them. Cars that got dealer-installed air used the standard pump, and added pulleys to the crank to drive the AC compressor. They would also install a fan shroud if the car didn't already have one. If Ma Mopar thought the standard water pump would suffice in this situation, who am I to argue? If you can't find an AC pump, don't lose too much sleep over it. Or go to Flowkooler and get one of their pumps.
What style pump to go with? The early iron pump is shorter, so in situations where radiator clearance can be an issue, I would go with that. If you have extra room, go with the later aluminum pump. Ultimately, go with the one you have the pulleys and accessory (alternator, power steering, AC) mounting brackets for, since each is unique to that style pump.
Lastly, if you want to run the early pump and don't have a timing tab, or are using a late timing cover, just make a tab. It's a bent piece of sheet metal held on by the 2 bottom water pump bolts- nothing exotic.
Just make sure the timing marks on your balancer are correct for whichever style timing cover you use.
