Does this look right
1973 CT3 wiring imgur.com/gallery/cJhULec

headlight does not blow out thank you for clarifying the wiring 

rectifier plugged into the 2 reds and red male goes to battery? imgur.com/gallery/QJnZyqI
fuse goes here? imgur.com/gallery/VAFnz2c

Hopefully someone with a CT3 will see pics and comment, the way the fuse is wired to a harness coming up behind the oil tank doesn't look familiar to me but it could just be routing or my memory? 

I missed your answer on how you're determining rectifier is going bad? 

One thing that doesn't make sense is headlight just "going out" and not blowing.  Headlight should only work with engine running and is not wired to battery or rectifier at all.  As I said before, a bad or disconnected battery can cause high voltage at the headlight which can blow the bulb...  but nothing in the rectifier/battery will shut off the headlight unless somehow headlight got wired to the battery? 

 

The first picture you posted (The one with A and B marked on it) actually came from an earlier thread on this site so unless you have a new username it's not a picture of your bike.  Several people responded in that thread that the wiring in that picture was correct. 



 

Yes mark that picture was a screen shot I took off this forum I could not find a pic anywhere but if this is correct I will follow his wiring thank you so much for all the help guys been driving me crazy for about 2 weeks I didn't want to cook anything

Looks like ya have to be logged in to see that Ct1 wiring link I put up, be it useful or not. The site picture link just doubles your text as I guess you've found out. I just link pics through Google photos but only end up with a link because I don't know what I'm doing lol. Imgur seems to be the one to use.

Actually your picture cleared up alot for me and helped me out alot couldn't find one pic of the underseat anywhere online

Is it possible the RED at rectifier connection is grounded outbound from connection? If this were true, then no short would occur until the engine was running and charging. Then after shorted, the lights would fail as their power supply would be grounded.

Just thinking out loud. Can't wait to see how this happened.

Not new battery with reverse polarity.
Had that happen once at work with a new acid battery 50 years ago, not a sealed battery.
In hind sight it might've been some noddy [not me that time] had filled it & put it on the charger straight from the fill but connected back to front so just gave up & charged back to front.
Not sure if that can happen but our super heavy battery charger with two big adjustment knobs would probably just grunt away regardless rather than short out & smoke lol.