I have heard that it will be very noticeable at low speed, easy to check, just make sure the u-joint bearing caps are lined up end to end:

http://www.4crawler.com/4x4/CheapTricks/Driveline-101.shtml#Phasing

I don't think it'll make a clunking noise, though. Usually more of the rough, uneven, pulsing feeling as it turns. Might be worth checking the slip yoke splines for damage, they may have been affected by the u-joint failure.