While doing a remodel at a clients house, I found/ bought a box of 73 CT3. I’m in the process of putting it together to see what I’m missing. This is my 1st CT3 and my biggest hurdle is figuring out the wiring after putting the engine back in the frame. It’s missing the right stop switch and the main switch/ key assy which I found on eBay.. my question is that I can’t find where to plug in the 3 wire plug?

Are you talking about the black plug with green, yellow and black wires? If yes, one end is from the left side handlebar switch, the other is from the headlight and they connect in the headlight bucket.

Just double check that the other part of your front brake switch isn't still attached to the underside of the front brake lever perch!

I wonder if you could be missing item 7 the headlight cord
 

Unfortunately its missing all the lights, front&rear brake light switches, and the rh handlewire stop switch. I'm mainly wondering where that round disc attaches to? It ties into the main wire harness, has 2 connectors and 10 different wires. I couldnt find it listed in Illustrated Parts. But on a good note I found a old coil, hooked it to the black wire, sanded the points and I have spark. Getting closer to see if It'll pop!

The "round disc" is the insides of an ignition switch.

You mentioned a right hand "stop switch" a couple times now...  it's clear now you don't mean front brake switch.  You're not missing a "stop switch" because the CT3 didn't have one other than the key.

You did show a picture of the remnants of front brake switch wires but no picture of the "three wire plug" you were puzzled about plugging in?

Ok, after figuring out the the round disc with 10 wires goes to the bottom of the keyed ignition and not the start/stop switch, i started looking for one on ebay. That 2 plug yamaha ignition is very hard to find. Looks like Yamaha went to a 3 wire ignition after 73, which i have one of those but wont work on a CT3. Lemme know if anyone knows of an alternate.
 

I seem to have misplaced a box of electrical stuff and somehow managed to break off the key to my shed while it was on my key ring...

Anyway, I'm pretty sure I have a few key switches, I will have to check.

Box was not in the shed.  I have a CT key switch with the ten wires...  rectangular plug with 6 wires and square plug with 4 wires.