When you say 'won't fire over' - does engine crank, just not light up?
If it doesn't crank, your battery is probably discharged - especially since getting no charging from that connector mess.
Did you re-charge it on a bench-top charger?
Does it indeed crank the engine over?
Are the headlights strong when you turn on the ignition?
Can you hear the Fuel Pump 'prime' (whine) for 3 secs after ignition first turned on?
What is the voltage at the battery when you turn on ignition & lights?
The charging system connector problem will not stop bike from starting, but you do need to check out both the stator & regulator to see if either of those is damaged.
Check out
this thread for a guide to diagnosing that system
Install the CBR FH008 R/R along with those recommended Metri-pack connectors.