Just a little update..
The trans is still very quiet.. Just an ever so SLIGHT whine, which was present after I picked it up. I would say that this is normal, and it has not changed at all over the past 1500 miles.
Going into 1st, and shifting from 1st/2nd can be just a little bit notchy when the trans is cold. However, I would say that this is pretty normal. It's not bothersome, and it goes away when warmed up.
I do have another issue, which is the rear end. The Ford/Lincoln technician that installed my OEM Ford 3.73 gears did a piss poor job. I have tons of noise back there.. from whining, to groaning when cold and going around turns. It also clatters and makes a hell of a racket from time to time. There's way too much slack between the pinion and the ring gear. I'm not sure if the pinion depth is off, or the ring gear isn't properly shimmed to make the correct contact. Or, it could be that the guy didn't tighten the pinion nut enough to properly crush the sleeve.
Either way, it's making horrible noise, and will have to be torn down. I think the pinion bearing is toast, and I'm sure that the ring/pinion will have to be replaced due to an abnormal wear pattern. I'm not taking it back to this jerk off, so I'll have to pay another shop to do the work.. AGAIN..
Sad.. I bought this car with the 3.31 gear, because I couldn't find a 3.73 car in the color I wanted with the options we needed. The idea was to get the car, and just put the OEM 3.73 Ford gear in, by one of thier techs, so that it wouldn't mess with the warranty.
I found a video of a guy that's having the same problems that I had with his trans making noise.. This is the EXACT same noise mine made. If you notice at the very end, when he shifts into 5th, the noise is GONE. Exactly the same as mine.