I have a 1999 7.3 F350 super duty. Recently I had the transmission flexplate replaced/upgraded, a new Torque coverter and filter. I then had a K&N air intake system and performance exhaust installed. Now I get a noise when the automatic transmission shifts back into a higher gear. It is most noticable when I am pulling a loaded horse trailer up hill. I get no noise when it downsifts only going back to a higher gear when I am accellerating???. The noise sounds like (okay I am going to do my best here) a small electric drill with a 2 second bust or a garden hose under pressure kinked with water sqealing through the kink. It only lasts a couple of seconds. I did notice it a littlesound going up a hill when the engine was lugging down a little. I was told that the filter is possibly missing a gommet of some sort and transmission fluid is under pressure making that noise when shifting higher. Any thoughts???.
I have changed the serpentine belt just to rule that out.

 

Having any part of the tranny upgraded, you will get enhanced noise from it. The E4OD already makes those noises, its just not noticable until it goes out, or has been beefed up. As long as you arent getting any slop between shifts, or hard shifting (really hard, as these trannys shift pretty stout) you are good. The K+N Air intake will also open up some noise (turbo whistle) and gets really noticable at higher speeds. Do you have a trans temp gauge? Thats suggestable. Get one of those, keep an eye on your temps. A change in temp with the noise will tell you a lot more too!