Digging into the wiring harness and a ign module ?

#1 son bought this non running barn find. He and I have went thru the carbs and verified good spark. We have hit it with starting fluid quite a bit and have only got a couple weak coughs out of it. We started disconnecting everything and cleaning the connectors we now have horn, turn signals oil pressure light, tail light. and both brake lights but no headlight yet with a known good bulb. The start switch is broken and local bike boneyard doesn't have one. I ohmed out the run/stop switch it's a simple two wire unit that shorts the two wires in the run position so that shouldn't be holding me back

I don't want to invest in an ign module until I'm sure that 's the fix and since I have spark I'm figuring it should at least start the bike. The ign module wiring harness looks to have suffered heat damage but from the outside not the wires themselves. We took the battery box completely out today and completed the connector cleaning. Attached is a pic of three modules located on the battery box.
I figure the box on the left is the regulator cause it's metal and heatsinked. The center box has three pins so it's most likely a condensor of sorts and the ign module is on the right. So if I have spark is it fair to consider the ign module good?

Left is the rectifier, middle is regulator, right ignition module.
If it sparks you're probably ok. Full check would be with it running with a timing light through the full rpm.

Some of the Yamaha right-hand controls will have a switch to turn the headlight on/off. Yours will probably not have one. My XS has a light switch, but my donor ‘78 bike doesnt have the light switch. I believe the headlight wire in the bucket is yellow, with an additional yellow powered wire coming from the hi/low switch.

If you disconnected the coils, the wires going to the harness could be reversed, making it fire 180* out. Are the spark plugs new? Did you remove the pickup plate? That will certainly change the timing.

Are you getting gas to the combustion chamber? Do the plugs smell like gas, you should need the choke to cold start it always.

Depending on the year the headlight comes on automatically after the bike starts.
I agree with what Newhaven Mike said. If you were cleaning connections you may have reversed the coil wires.
One easy way to check is swap the plug wires left to right.
Leo