I've got the creak pretty bad, also have the 3650 issues like not wanting to go into reverse and occassional problems shifting into second. Also the damn steering wheel shakes like a monkey on X going down the street. Only 20K on it. Taking it to the dealer when i get a day off 

Has about 6k on it and i have no squeaks or creaks. At about 1k miles i developed a bad creak where the dasboard and the a-pilar meet on the passenger side. Tried all kinds of things to try and cure it to no avail...Finally took it to Ford for warranty. It took them a week but what it turned out being was 2 missing welds behind the dash where the firewall meets the a-pilar. They tore out my dash completely, welded it like its supposed to be, painted it and put it all back together again. I was worried about squeaks and creaks from them tearing my dash apart but to this day(knock on wood) i have not had 1 creak or squeak from anywhere in that car. The tech who did the job told me what he found and said those robot welders miss tack welds all the time and inspectors miss finding the missing welds. He put the dash back together tighter than when he found it. This guy had a love for stangs and really did the job right for me....
. The first year is usually the test bed and has recalls and problems. Not all, but some. Like the 99 Cobra
. They usually iron these small problems out by the 2nd year model.