Yes you should replace the rod if it is shorter than 3 1/4" but the pump should still hold pressure with a rod up to 1/4" shorter & if it dosn't you have other problems as well.
If all else is good & you are getting a full stroke on a good pump it will run down to about 3/8" shorter than the factory 3 1/4" without loosing pressure. There will be hundreds of bigblock owners out there that needed to change to an electric pump because they were using too much fuel for the mechanical pump when they only really needed a full stroke of their mechanical pump.