That's what I've heard, too. A Diablosport Intune I1000 will run you about $290, and it can download custom tunes from the web and install them on your ECU. Another handy feature is that it can turn off MDS (which a lot of people find to be kind of an annoyance). You might be able to find a shop that will do it for you without buying the device itself. Might be worth turning off your MDS, as a part of your troubleshooting efforts, but be aware that you'll probably see a drop in your MPG.
If you have custom exhaust and still use MDS, that might cause a drone. I've heard about guys who have deleted their resonator and get an obnoxious drone at highway speeds.
(I, myself, plan on cutting out the stock muffler and putting in a Flowmaster Super 44; haven't decided on deleting the reso yet, but that's for another thread.)
Hope I could help, and best of luck!
2005 JGC 5.7L
stock... for now 😉