no spark

bike is a kz 900,bike was runnin good took in for a valve adjustment/tune up,and to have it dyno'd,picked up bike it was running fantastic on the way home it started raining so bad it was like i was in a car wash,on this bike there is no factory switches for lights,starter push button,kill switch they have been replaced years ago with after market switches,the ignition switch is still factory,they are all exposed to rain ect ect, when i got home i parked bike still pouring rain all thrue the nite,next day bike was stone dead just gave a click click,charged battery,battery was low so i pushed started it bike started rite up,found bad starter solenoid replaced it,attempted to start bike, bike would not start but it cranked over but would not start,then discovered the starter wire from solenoid had been pinched from the engine cover and was grounding we repaired the wire the tried starting bike still would not start found we have no spark,at all and we do not have power at the coils at all,this bike has dyna coils,dyna minder and a square box that says dyna that has 3 controls and a hi/lo switch, we also found a resistor in the line supplying the coils,our questoins can and should the dyna be by passed if so how? could my ignition switch be the problem or the reg/rectifer? please any help would be great.

id start at the battery and follow through your connections to see if something got wet and shorted,have you checked fuses?

yes i have checked fuse's
what ever did happen it killed the battery,after charging the battery overnite it still would not crank the bike over.