yes, you can program window opening via the key fob... i did it and it works well... you might also look at the spreadsheet and do the window reset if your windows are not opening and closing right (doesn't require forscan, just a little trick with window buttons)..
got my 4 door FE in october... did you call brian nugent? and did you confirm with your salesperson that they put the order in (via a sales order sheet).
Happened to me too.. I did the window reset which fixed for me… for the windows causing issue open it and hold button down for ten seconds, then close and hold button for ten seconds … repeat two more times … this also fixed my rear window which wasn’t functioning properly when door was opened...
i removed the accessory panel and put in the garage and so far i haven't heard the noise again... will by driving 3 hours tomorrow and am leaving it off so will update ... if that is it, i will try some stick on felt and resin tall the accessory plate to see if that solves it...