[Puck Luck]

Phil is spot on about repacking/rebuilding joints. Rebuilding outer joints would figuring out what was worn. The balls, the cage that houses the balls or the joint housing itself. Would need some funky measuring tools to measure up some of that, and compare to the original specs. I wouldn't even know where to find specs on that sort of stuff. Maybe a machine shop that specializes in cv joints?
But i do have a slightly different opinion in regards to "bad shafts". I've seen quite a few new or re-manufactured aftermarket shafts, right out of the box cause vibration while accelerating. Even some high mileage eom honda shafts.
It's very difficult to try and figure out if its the left or right side. Not really an exact science. Drive with the wheels off the ground and lock one wheel at a time and try to see if one is causing a vibration. Not always easy.
Nor can i say i know if its the inner, outer joint or the shaft itself causing vibrations. (although i suspect it may be the inner joint causing it). I doubt the lack of damper on the shaft would be an issue.
So to answer your question, i think its the aftermarket shafts causing the vibration. Especially if it wasnt there before. If everything with your car was reassembled correctly, then i highly doubt its an alignment issue