Yes, the EGR could cause the MDS to hunt. Do you have any of the MDS symptoms......erratic, (sometimes almost stalling) idle, surging at ~35-45 mph, and/or poor fuel economy and performance? Sometimes the EGR will be going bad and it will not throw a code. Before purchasing one, just make sure it's not a Chinese unit. A couple years ago, I bought mine from O'Reilly's and it's been fine. In addition to an EGR Valve tester, I also have a way to monitor mine onboard to insure proper function. Let us know what you find.
There is no learning process for the new valve and the job is not too bad. If you cut about 3/16 in. off the bolt that is hardest to get out (as I recall it is the inner one that hits the alternator), next time it'll be even easier.
Remember, among other things, the MDS is very load sensitive, so anything that causes additional drag (brakes dragging, low tire pressure, wheel bearings, racks, a lift, etc.) will have some affect on its operation. On the highway, mine is normally on in excess of 90%, but then mine is modified quite a bit.
06 GCO, Dk Khaki, QDII, Flshing Hi 3rd Bk Lt, MDS "ON" Lt, Airtab Vortex Gens, Debadged, Fumoto Drain Valve, BT Catch Can, Chopped EGR Tube, SRT8 CAI, K&N Filter, Sonnax Trans Line Press Booster, SC Tuner W/Adv Trans Tune App, DS Tuner, Cust tubular hdrs w/3 in Magnaflow/Xlerator AP Exh Sys, Bilsteins, SRT Springs/Sways, Cust Eng Cvr, SRT8 frt/rear bumpers, FRI Sidewinder Cam/6.1 valvetrain, SLP 25% UD Pulley, BBK true 90mm T-Body, SOS Ign Coils w/.060 spark plug gaps, SRT Reps with 265/45&295/40X20's.