Slight "surging" / jerky running 07 ec450fsr

[Why Z?]

Hi, bike starting fine (issue seems resolved with learning the bikes "personality")
Running mostly okay but a couple slight issues:

1) bike is a little hesitant/boggy in 1st from a stop, and between 1st and 2nd when accelerating
2) at "cruising" speeds on roads for instance, I notice that it sometimes hesitates/surges while the throttle is held constant. For instance I will be cruising at say 45 mph and then after a few seconds I will get this "ht" outta no where. Not uncontrollable but not "NORMAL" either.

3) One day I took it out to warm up before changing oil, it was after dark and after running/riding it maybe 5 but less than 10 min, (in the dark) I looked down and noticing the header was starting to glow RED. NOT BRIGhT red, but glowing a bit.

What could be causing the surging/nt smooth running?
Too Lean????

Also, bike came w 2 ECU's, not sure why though and Prev. Owner wasn't sure . (It was a research bike for the company he worked for).

'07 EC450 FSR
-I have had bike for about a few wks now
-bike has very low miles (fresh rebuild when I got it)
-gas: 91 Pump gas non-ethanol (non dedicated pump though)
-oil/filter: Rotella T6 5w40 ("full synthetic")
changed twice since I had the bike (prob about 2 hr apart)
-air filter: when I first took out to change after a dusty ride, found a tear near the seam where it seals to the bike. Now have a UNI (seems SUPEr bulky) and a FLO (seems to fit better). Did the no toil on this one(I tend to over-oil a bit maybe w regular oil)