440 mounted with a motor plate in a 67-69 Dart

There are a couple of ways to make a stock type water pump work. If it was me, I'd mill the back side of the water pump housing down 1/4 inch and then use a .125 spacer behind the crank pulley. That gets everything back into proper alignment with a 3/8 motor plate.

The alternator mounting is another issue. I have alternator bracket kits for motor plates, but not for use with a stock water pump. I don't know anyone who sells a kit like that. I've built them before so it can be done, but it does require some fab time. I run a motor plate in my car with a belt driven water pump and a 60 amp Denso alternator. It all fits and works just fine but it isn't "off the shelf" parts.