OK, I think we fixed the problem. What we found was kind of weird. I want to explain it just in case someone else has the same issue. First we check all of the connestions around the throttle body and they were clean, no corrosion, ect. Just in case and for future protection we coated the plugs with dielectric grease. Next is where we found what I believe to be the issue. We removed the front part of the fairing and found the fly by wire connector that comes from the throttle itself. We removed the assembly from the right side of the handle bars (switch cap, master cylinder, brake lever and handle grip). The purpose was to check all of the connections within the electronic throttle wiring. When we unplugged the lower connection water ran out of it. It seems that the protective cover around the wiring was placed in an upward position in a way that it would catch water. We pulled the throttle assembly out of the handle bar enough to reach the protective cover the took and air hose and blew air through the cover. We also blew the connectors dry and cleaned them, the lower connector that plugs in behind the fairing and the small 4 prong connector that is found within the handle bars. Dielectric grease was applied to all of the connectors. we also siliconed the ends of the protective cover as to not allow any water to get in it again. Everything was reassembled. I took of for a ride of about 30 miles and didn't have an issue. Going to take a longer ride tomorrow and see what happens. I hope this helps someone in the future if they have the same issue.
Also here's a hint... If you remove your outer fairing check and see if a corrugated plastic cover, approximately 1" in diameter on the right side, is laying across the steel fairing brace. If it is try to position it off of the brace. Over time viabration will cause the steel brace to wear thru the corrugated plastic and eventually the wiring thats found inside. Needless to say, if this happens, you will have an electrical short.
Thanks to everyone for their comments and suggestions...