Use the AR-Engineering plate, it's nice. I use it along with a stock type water pump housing, I haven't had it milled because my pulleys line up good. But I only have 2.75 inches between the water pump snout and my radiator, so I use a cheap flex fan along with a shroud.
I use a Toyota Denso alternator and will never go back to a mopar setup, it's small, mounted low, and charges at 14 volts at all times, best setup I've ever owned. I'm sure alot of guys have the mopar setups ironed out but I always had problems with them.