I can answer a few of these:
-Its very possible that the blend doors that are faulty, it is a common issue with the WJ.
-The noise after shutdown, moving the doors? that's normal, no worries.
-Never worked with the fan system, hopefully someone can chime in.
-There's a common issue with the heated seats, here's the pdf of the tsb: http://www.wjjeeps.com/tsb/recall_J14.pdf
, that's one possibility as to what's wrong. As for the switch lights, you may be able to repalce the bulbs, but i've never seen a part number. May be worth it just to get a couple switches from a junk yard assuming your wiring is good.
-As for websites with oem part numbers, i practically lived on http://wjjeeps.com/
during the first month of ownership. http://www.factorychryslerparts.com/
is probably closest to what you described.
Also, fill out your jeep profile so we know exactly what model, engine, trans, etc. you have