Welcome to the site !!
Do you by chance have the Owners or the Factory Honda Service Manual ??? , it has all the correct readings for the Stator , Coil , to see if they are within spec , you did not mention if the "readings" were correct or that you confirmed this , or if you just checked to see if they were getting power , so we need to know the details , as there are a lot of variables ...... Intermittent spark can be from many things , including the Stator , or even the spark plug boot itself or even the CDI , but what concerns me is the issue with the burnt wires , you said you repaired the wires , but the issue is , what caused the wires to melt ?? , something either was shorted out by way of wires getting the coating rubbed/worn off and shorting , or the wires got too hot for some reason (could be many reasons) , and possibly overheated the CDI , Stator windings ,or compromised a ground wire ....
The ground wire at the rear of the engine right behind the clutch actuator sometimes comes loose , it looks like it is still connected , but from lifting the subframe it can become loose in the connector and without that ground , the bike won't start , or run very well if it does start , because of a bad ground , pull gently on the wire right at the connector where it is screwed to the engine case , and see if the wire moves in/out ....
Did you trace the wires ?? , if so where did they go ??? , Stator ?? , CDI ?? , , and if so did you test them specifically ???
When you are testing outputs , are you using the starter ?? , or the kick start ?? (kick starter by hand ??), is it turning over slowly ?? , as that can affect how the spark shows up , are you grounding the plug when starting it ?? , or is it just lying on the head or valve cover ?? , as that could give a inconsistent reading ...... The more info you give , the easier it is to diagnose .......