Is there a way to check what the check engine code is on a 6th gen accord without using a scan tool? I can't seem to find the service connector to short it and read the flashes like on older Honda's.

 

You can't, this is an OBD-2 system, and as such you need to use a compliant scan tool to retrieve the codes.

 

in the passenger side kick panel where the ECU is there is a two wire connector plug...
it's not plugged in to anything..
it should have a dustcover on it though..
find it....
put a jumper.. or wire.. or paper clip or something conductive in the two holes...
then turn the key to the on position

the Check engine light will flash..
Long flash = 10
short flash = 1
so
Long Long Short = 21
then look up the codes
http://www.hybrid.honda-perf.org/tech/codes.html