I put an AFE catback exhaust on my 03. At first it wasnt much louder than stock, but when towing at around 65 - 70 it just whines and leaves my ears ringing by the time I get home! Is there any way to stop this or do I have to go back to stock?

 

make sure you have the tip out well past the bed wall.

look from the rear, and your tip should be past the wall, or it will resonate.
if the tip is facing the trailer, it can resonate.

what kind of trailer?
my flat front 24 would echo pretty bad when pushing the pedal, was Ok at cruise though.

i would put a small muffler up where the cat would be.

if you could get an over the axle resonator off an 06, you would be in business, but not sure how much straight pipe they would have on the end to use to connect.

but you can get a small (~24 inch) muffler cheap.
http://www.donaldson.com/en/exhaust/...ent/index.html

 

I agree with 04ctd about the resonator. I put an additional short muffler ahead of my Magnaflow 30" to smooth out the drone. Worked out great!

Do you still have the CAT installed? If so, that should already be acting as a resonator already. Then maybe check out getting a 30" Magnaflow to replace your AFE muffler.