to the forum cboyslvr91903!
Losing function in all 4 windows rules out motor failure in the doors, so the most likely cause is a bad window switch in the center stack
Your second symptom needs a bit more information for us to make an even educated guess at to what is going on. Describe the noise please, is it a mechanical sounding noise, or a thump, or both. Also, have you ever experienced leakage of water into the passenger side foot-well?
There is a rubber patch/membrane under the cowl on the 2006 and early production 2007's that is notorious for leaking water into and behind the dash, that may be the source of your problems.