When I went to put in my LS1 aluminum Driveshaft, the end caps slipped off my u-joint. Is this normal? Am I going to have to replace the u-joint or can I repack the bearings and place the caps back on?

 

It's normal, it's something that you need to be aware and careful of.
It's no biggie though. If the pins aren't disturbed just carefully put the cap back on.
If the pins are out of position use some grease to on your finger to stick them back all in a nice neat row then put the cap back on.