I don't think there's too much to the carrier bearing alignment- your problem is likely elsewhere. Check the t-case and pinion flanges for looseness, spin the shaft and check for any wobbles, re-check the u-joints for any looseness, make sure the CV is solid, etc. The driveline shop should have checked all that for you though. And if the shaft is really twisted, it is probably weakened and will only get worse and should be retubed or replaced.

'97 4Runner, '06 F350, '86 4Runner, '05 WR450
http://home.4x4wire.com/erik