I had shims on a couple of Legacy diesels for years, I eventually sold the engines, but the shims were still intact and working. The shims were to correct the axle slop that actually allowed the gears to move enough to slip teeth, never had the problem after I finished a couple loaves of bread. 
As far as synchronizing different cruise methods, I think that's going to be pretty difficult in any case. Remember, the speed graph on the Legacy controller for R100 is not calibrated in scale MPH, as the patent for indicating scale MPH is held by MTH. Retrofit cruise installed after the fact is simply not going to consistently match up with any factory cruise as a rule.
What the ERR Cruise will do for you is allow you to maintain a steady speed on straights, curves, and grades. I have the same Allegheny that I upgraded to ERR Cruise, it's like a different locomotive.
