If the mechanic that replaced the throttle body performed the relearn, the shifts probably aren't related. Throttle relearn will have more of an impact on idle if anything - at least in my experience. Replacing the throttle body will take care of P2135 and the subsequent engine power reduced but it won't change the transmission shift quality issues you've described for a long time.
Now if it is worse than before... it could be a) the relearn actually wasn't done or failed, b) the transmission clutch adaptives are so out of whack from the failing throttle body they are poorly learned, or c) the properly learned and working throttle body is exasperating the previous transmission shift quality. If the problem you describe continues I'd drive to 500 miles or 1 week (don't wait too long) and call the shop. They can scan for codes, learn it again if they think that might help or perhaps forgot, or run the adaptive fast learn on the transmission.