Just a place to jot down varius issues i ran into, hope they help the next person!
Some injectors not firing:
First array element in H[2] not firing. manually triggering the array output using mdh command. All other array elements worked regardless of output.
this is discussed briefly on the bottom of this page GenBoard/Manual/DigitalOut
From what i found, alot of the misc outputs were set to injector channels. I opened up the Megatune and opened the tab for all outputs table. Most of them i wasn't using, and i just set them to disabled.
This cleared up the issue - but boy was it a pain to figure out.