Has anyone else had this problem?

I just recently noticed that I have a faint but noticeable squeak coming from the engine bay or surrounding area. The squeak is not continuous and only occurs when you hear the auto tranny getting ready to hit 3rd gear, It sounds like metal against the chassis, however i can't confirm that. I had the AEM short RAM which for some reason seemed to make it even more noticeable. When I'm in a lower gear or low speeds it never makes the noise, until I speed up and the automatic tranny decides to make its way into 3rd. Also on a few occasions i have also experienced a slight bit of difficulty in moving the gear selector out of park into drive, and when it is in gear it is followed by a thump or a thud. I live in Florida, so I know it can't be cold weather. I just would like to know if anyone has had any similar issues with a 01 es automatic? I really hope it has nothing to do with the transmission! Please Help!