Marking the flanges should not have been needed, I always do just to be safe, but I am anal about some things. Some people have been posting lately about getting bad OEM guibo's out of the box, seems they are hard as a rock and do ot flex the way they are supposed to, maybe you have one of these?
Can you tell where the noise is coing from? sometmes driving down an alleyway with building crowded on both sides can help locate noises. Try driving with the windows up and the windows down, rear window up/down etc. If it makes noise inside at 20mph, there is a good chance you can hear it at 10mph or so if you are in a narrow alley.
An out of balance drive shaft should not vibrate until higher speed, low speed vibration is a sign of binding. Might be worth double checking the carrier bearing is aligned properly. Also make sure its faceing the right way, the mount can be put on backwards.