If I were the Honda dealer, the first thing I would do is have you remove all the aftermarket stuff and see if that cures the problem. If you dont want to do this, then drive it like it is. Aftermarket crap is cheap at best and probably was installed by a bunch on high school kids working for these places. And since there are few 06 hybrids out there they probably for sure on this one did not know what they were doing. It should not be the Honda dealers responsibility to fix the car after you let other people jump in and put the aftermarket stuff on there. Tough words, bite the bullet and take the aftermarket stuff off and see if car works right then, if not, then hope that Honda will warranty the thing. I'll bet the stuff you added was NOT for a HYBRID model, rather a plain old CIVIC....two different cars. Good luck!