the motor is a '68 396 + .030, i'm planning on using an aluminum flex fan and my big Afco racing radiator.

What is the difference between the two and which one do i need?

Long water pump is called for brackets alone are a lot easier to find
Since thats the way it come should be no clearance issues.

it's a good idea to use the long style pump,
the brackets and pulleys are easy to find off many donor vehicles,
the 68-cars had short water pumps for both sb and bb as stock.
you will want to use a 69-72 radiator shroud with the long pump
you could use a 68-shroud but it will need trimming in a couple of areas depending on if it is bb or sb type.
the area by the alt and crank pulley had to be trimmed when i used the sb shroud on my bb.
the alt harness will also need to be extended it you move the alt to pass side of engine..... :)

I agree long water pump.

Brandon I have the short W/P on my 396 go LONG!!!!

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What is the difference between the two and which one do i need?

The difference explained: http://www.chevellestuff.com/tech/water_pumps.htm