Reading about your last attempt, I am assuming your bike is carbed. The symptoms that you have described could also be an issue with ignition timing. I am not sure how ignition timing is calculated in a carbed bike. Does your bike have an ECU? On a different note, these could also be symptoms of ISC lines being disconnected and throwing off the AFR.
I have sourced GV650 coils off of ebay, which are a little longer in size but have the same orientation of connectors and come with new plug cables and caps. (http://surl.li/sfsix)
I was unable to remove the temp sensor from the bike last night, for lack of a better tool. Once I get it removed, I want to check the voltage being produced by the sensor under different temperature settings and compare them to the default values given in the repair manual. Today I am doing a resistance test on my old coils and will update you on that soon.
Sam