Issac, the o-ring to seal the float bowl does not go onto a "jet". It's a part with a groove that Yamaha called a "jet setter"

The main jet is supposed to be located in the end of the jet holder that threads into the side of the float bowl. 

See parts diagrams

Mark, I have attached some photos below. I looked at a parts diagram but dont seem to see the small o ring that goes into the small hole in the float bowl. I believe its for the starting circuit (choke). See the first image below. My second question is about the primary jet. The original seems to have any o ring that goes around it. I purchased a 150 jet as a replacement but it does not have the groove for an o ring. Is the o ring necessary? The difference in jet sizes from OEM (can't find any stamped size on it) to the aftermarket 150 I purchased are huge. 

Images: photos.app.goo.gl/h8n6j9hCYYmrCoyg7

No o-ring goes in the hole you're pointing to in the first picture.  That's the well the starting circuit draws from.  There's a tiny (non-removable) jet at the bottom that regulates the fuel for the starting circuit. (Starter jet)

And again, you have the main jet installed in the wrong place.  The jet setter that takes an o-ring to seal to float bowl goes where you have the main jet installed.  You are holding the jet setter in your hand along with the pilot jet. 

Jet setter:


Main jet goes into end of the main jet holder that screws into the side of the float bowl so you can change the main jet without removing the carb.  You do not show the main jet holder in your pictures.  It looks like a float bowl drain plug. 

Here is a picture of a CT1 carb with jet setter and o-ring.  Main jet holder and main jet are in the upper left of the photo.  Jet screws into end of holder, holder screws in to side of float bowl.

Mark,
Thank you so much for taking the time to explain that to me. I understand where I went wrong now! I will report back in a few days when I get it back togeather and hopefully start the bike.

Thanks, isaac

Mark.

Just to muddy the waters, there do appear to be two options for the setter jet - see the two "5" items on the attached. I wonder if the early setter jets didn't have the 'O' ring (see what I assume are the VIN numbers alongside the two different parts)?

Yamaha AT1E 1969 USA CARBURETOR - buy original CARBURETOR spares online (cmsnl.com)

Both had o-rings.  Early type did not have a groove, it was a "jam" type.  The pictures of Issac's carb looks to show the later type with the lip at the edge to retain the o-ring.

Why not just buy a selection of small size orings from ebay and have some spares?

Thanks Mark! 

Mark,
    I have one more question but I think I may be paranoid. My jet setter is a bit chewed up. From photos I've seen on this site as well as new jet setters I can find online, my jet setter looks a bit larger. I have inspected it the best I can and I don't think it has been drilled out. The ID measures about 2.6mm. Does that sound about right? 
photos.app.goo.gl/57Pe2i6dYvJSt3W7A

Thanks,
Isaac 

It's not a calibrated hole...  it needs to be much larger than the main jet that is calibrated.  You'll be fine as long as the o-ring seals into the float bowl. 

If the o-ring leaks or is missing, then the fuel will bypass the main jet in the jet holder. 

Here's a trick you can do on the early AT and CT....  if you have an issue with the oring seal, install the main jet like you had it before and leave the o-ring out.  Bike will run fine, you'll just need to remove the float bowl to change the main jet which means carb removal.  If you do this, you can either leave the jet setter out of the carb completely or install it (without o-ring) on the end of the main jet holder.

I had some crap plug a pilot jet out on the trail once and the o-ring got damaged in the process of removing the float bowl to clean it out.  Installing the main where the jet setter belongs saved me a long push home!