I did a stage 1 with new head pipes on my 2015. It seems to run cooler than my 2009 stage 1 with lowers.Stage I kit will do wonders for cooling the bike down.
The rough running at idle when warm is probably the EITMS kicking in. It will shut down the rear cylinder at idle to help keep the engine cool. Makes it idle funny but is totally normal.
+1 on the EITMS. Mine came disabled. When I enabled it, I noticed a significant difference at idle.