there is a pump alingment tool
unless you have removed the engine for some reason and didnt keep the factory motor mount shims in place , you should be ok.
if you are just replacing the shaft, then no alingment is needed
plus the pto side of shaft is crowned a bit to allow a little mis-allingment.
i would loosley put shaft in with pump and check to see if shaft shoots straight for pto hole, should have the carbon seal and slip ring in place, leave the c-clip off at this time, your just checking alingment at this time.
so with pump and shaft sliding in, it should pretty much head right for the pto hole and slide in! at this point slide the silver slip ring against the carbon seal at make sure it is sitting nicely against each other, if all looks good then pull back apart and re-assembly her for good.
if not, get a idea were the motor needs to be moved to and apply shims under motor mount to bring engine into alingment with shaft.
mud