Hello everyone just finished a full restoration on one of my 1973 ct3s I'm having a hard time figuring out where the rectifier and battery plug into ive blown 2 rectifiers headlight works for about a ride then rectifier goes out upon inspection of my other ct3 I notice the 2 reds going to rectifier but that bike was purchased with no battery can anyone help by uploading a pic with how the connection goes thanks in advance guys.

Welcome from NZ. Here's a color 'colour' diagram link from the vintage site but for a CT1 which would still be relevant 'enough' i would think, but hope someone comes up with the correct model diagram.
Anyhoo--it shows a white going to the rectifier from the switch which i think is always the case & my understanding of it 'is' that different rates of charge are linked through the switch for daytime charge or night depending if light on or off.
Regardless of all that, even if you ran the highest rate of charge straight to the rectifier--ie yellow straight in, all you'd do is boil the battery dry in a shorter time but i still couldn't see it roasting the rectifier.
Red goes straight to the battery from the 'out side of the rectifier but looks like it T's off to the switch--which i guess it has to so as to battery power things like horn, indicators, brake light etc.www.yamaha-enduros.com/index.php/wiring-...ct1-c-wiring-diagram
I'm guessing your 'headlight' is running off the magneto & not the battery by mistake.
In the US i 'think' & might be wrong, that the tail light runs off the battery. But in NZ ours were wired with headlight as that diagram link might show.
Possibly though early models like yours were still magneto powered tail light like all our models were through the years.
Sorry i'm wondering & woffling on haha.

A picture would really help if anyone has one of the underseat 

A picture of what you have would help us too.

I'm also not clear on what you're describing...  Headlight is burning out? 
Or rectifier is burning out?  Both?

What style rectifier are you using?  The old original large "plate" style or the more modern little black rectangular diode type?  It's rare for a rectifier to blow unless the polarity is reversed.

just the rectifier is burning out but the headlight goes out once I put a new rectifier light works again. I'm trying to upload a picture of what I have but site is not allowing it. I have 2 identical CT3s but both have the red wired differently I did a full restoration of one and unfortunately the tape labeling the red wires came off and can't recall but basically just trying to figure out what red lead on rectifier goes to and what lead battery goes tojust the rectifier is burning out but the headlight goes out once I put a new rectifier light works again. I'm trying to upload a picture of what I have but site is not allowing it. I have 2 identical CT3s but both have the red wired differently I did a full restoration of one and unfortunately the tape labeling the red wires came off and can't recall but basically just trying to figure out what red lead on rectifier goes to and what lead battery goes to 

Rectifier "burning out" should not make headlight go out and then work again after replacing rectifier.  Headlight is not wired to the battery or rectifier...  (though if rectifier or battery goes bad the headlight could burn out due to excessive voltage...  but headlight won't work again if it burns out)

You need to upload photos to a third party site like Imgur and then link them here.

Rectifier wiring itself is pretty basic.  White wire and red wire. 

I'm beginning to wonder if you're talking about the fuse or something else and not the rectifier?

100 percent the rectifier not the fuse part number 315-81970-61-00
ran through 2 of them since the restoration assembly the wiring diagrams are a pain to make out.
I must be plugging the red wire from rectifier where it doesnt belong strange thing is when new rectifier goes in headlight works for a little then rectifier goes headlight goes aswell. I tested the rectifier and getting 0 ohm reading 

That's the weird part headlight works again once new rectifier goes in. The harness near the tank has 2 red wires with 1 female plug another red wire with male plug then coming from the rear fender i have 2 red wires with individual female plugs. Thanks for your patience guys I'll upload some pics once I get back home. I did find a pic on this forum of how everything plugs in but that user was having problems aswell I will post the pic just to confirm his is right

Is headlight bulb burning out and you're replacing it? 

Or is headlight just "going out" and working again once you replace the rectifier (which is what it sounds like you're saying)? 

Rectifier should have zero or close to zero ohms in one direction (not "OL") and some reading in the other when you reverse meter leads. 

Red is battery and white goes to stator.  There's really not a way to hook up a "wrong" red.  They all go to battery.  People do get confused on the battery area having three reds, two females go to the fuse holder and male goes to battery.  If you have battery power at the red you're connecting to the rectifier that is correct. 

You didn't answer about which rectifier you're using so I'll guess it's some kind of aftermarket replacement?  Red side should be marked + and white side should be marked with a squiggly line ~

There could be a bunch of reasons you are having this issue like someone could have assembled the ignition switch incorrectly or something.  Need some clearer answers about exactly what happens to headlight and exactly what happens to rectifier (how do you know it's bad?  Before and after readings?) and maybe photos to help figure it out.