Yes, your local auto parts store should carry a variety of shims and if you purchase a new starter you typically get a "base" shim included.
Not exactly what you're referring to by "alignment." If you have both both starter hold bolts properly torqued down then the starter will be where it needs to be. You'll want to make sure it is torqued to proper specs because a loose starter can cause physical damage to the engine block from starting jolts. You can then from there just adjust whatever shim sizes you require if there is mechanical starting issues with the car. I compare mounting point and starter wheel sizes first from the old to the new unit, reuse the old shim first, and then if shim adjustment is needed remove the smaller bolt all the way but just loosen the larger hold bolt. Then shims can simply be slid in and out with the starter in place.
To add also, the shims that usually come with new starters are pretty thin. They're almost more like "covers" more than any sort of actually usable shim. Another thing I do as well is clean the old shim(s) so any and all crud is off of them, since there could be crap on there unevenly and thus mess up the clearances when you reinstall.
[This message has been edited by Fiero84Freak (edited 04-19-2012).]
