No, the stock alternator will not fit anymore in the stock location. You have to hang it below the plate or come up with some other arrangement.

The stock water pump will work fine once you adjust the pulley depth. You can either space out the lower pulley using the 3/8 spacer that Mancini sells, or you can have a machine shop mill off 3/8 on the back side of the water pump housing.

Most guys using motor plates are serious enough racers that they don't mess with stock accessories. They usually run electric water pumps and racing alternators. But there are kits to hang small alternators on the motor plate. I make one of the kits myself and DMI has a low mount bracket kit also. So there are options out there.