Pulleys don't line up

There are water pump shaft spacers available for spacing out the water pump pulley.
http://www.speedwaymotors.com/p/611,33_Water-Pump-Pulley-Shim-Kit.html

As far as the alternator is concerned, put two .250 spacers between the alternator bracket and water pump then put one .250 spacer at the back spacer at the head. Your alternator is now .250 farther foward.

Chuck