I replaced one of my front struts yesterday with one of my new kyb struts. Now the front end thuds. I know all of the rubber and plastic assembly is bad and i need a new strut bearing. I also know that i am in desperate need of an alignment. Could the thud just be coming from my wheels being so far out of alignment or could it be all of that assembly rotting out?

Alignment can't cause a thud. All your bushings, and especially the strut bearings, being bad can.