Ok, so I have an the CVO 103 kit on my bike (see below for bike description) and ever since I did this install it seems as though my bike overheats a lot easier (and more often) than it used to. I can only recall one time when it overheated with the stock 88ci motor, and now I think it has overheated 5-10 times. When I had the stock ECM in the bike would go through the standard overheat protection procedures (cut out one cylinder, dump fuel, then shut down the bike entirely until it cooled) but now that I have the Zippers T-Max it doesn’t do that, I only get the "Check Engine" warning light and at that point I panic because I wonder how hot the motor really is. Sitting in a traffic jam is really the only time this has happened, but I cannot let this go on I have to fix it. I am taking a trip to southern Spain this summer and I know it will be EXTREMELY hot down there...so this has got to be fixed by then.
By the way, I have just installed (but not hooked up and configured) the Autotune, so I am hoping that this will help. But, what if it doesn't? Can anyone tell me what else could cause this? I ride with others who have high compression 95ci and other builds and they don't have this problem...

2003 HD FLHTCUI
SE 103ci CVO motor kit (stroked 95ci w/SE103 Heads)
SE 6 Speed transmission
Zippers Red Shift 575 chain cams
Zippers Adjustable push-rods
Zipper High Flow 2.75 breather kit
Fueling lifters
Delkron Cam Support Plate
S&S Oil Bypass Valve (to remedy oil blow-by in the air filter)
Cometic .030 head gaskets
Thunder-Max ECM
Autotune (both Gen 1)
Supertrapp 2:1 Supermeg
Running HD Syn 3 in all holes.
Thanks for any help!