I also think that you will have less cooling with Love Jugs fitted rather than the admittedly ugly but effective standard cooling fan and shroud. The standard set up helps with cooling the rear of the cylinders on the move and Love Jugs won't. If you have 569 cams then NGK DCPR6EIX plugs are recommended rather than the 7's. A check of the ignition leads, particularly around the edge of the bonnet cover is a good idea.
You can read the history of your engine with ProTune 2 recording the max cylinder temps and peaks on recent runs, that will tell you if you really are getting some exceptional temperatures or not. I cannot remember what my peak figures were the last time I looked but most trips were fairly constant. I really doubt that your running issues are caused by overheating. Probably different in the USA but in the UK over cooling seems to be more of a problem for most of the year. I have an oil pressure and temperature gauge that gives a good indication if things are getting hot. Even on a hot (30c+) day the oil temp rarely gets over 110c and the engine runs steady at that.
Sadly we don't have a knowledgeable S&S ECU tuner with a M3W compatible dyno at Krazy Horse or anywhere else in the UK now either. Not many dealers that know there stuff with M3W's here, so the "every sniffle" 😁 option doesn't exist either and I doubt things will improve with the end of production.
