Shami,
Kick ASS write up!
Couple points:
1) Rather than cut the defroster venting, just cut the back corner off the radio tray. it won't hurt anything at all and there's no risk of inadvertent 'slip' damage. I cut off all the trays for wire clearance when I do Avic installs. Never a problem.
2) If there's a hum, there's a loop somewhere. I theorize that a ground which is normally looped through the changer due to wiring -12v to mounting to the chassis is, of course lifted since the iPod is on no way grounded to chassis. To cure: You may try grounding the actual exterior of the stock head unit chassis. You may also wish to probe the harness for the -12v signal in the former changer/now iPod harness at the stock radio and ground it, thus simulating the factory loop.