So my new carb bowl gasket seems to be holding ok now, I don't see any more leaking from it. The aluminum crush washer still drips a tiny bit but the replacements I got online were not OEM parts and were too small.

The main issue I'm having now is the bike is fouling plugs. I put in a new B8es plug and it fired up great but after just a few minutes of riding the bike crapped out and the plug was black and wet. I have cleaned it off and fired it back up a few times but it keeps happening. Choke on, it fires up, gets to operating temp. Once trying to ride it feels slightly sputtery until about 2500-3000 rpm then it wakes up and pulls like I remember. Once I start coasting down with no throttle it sputters and dies then won't restart. I backed the idle mixture screw out another 1/4 turn but it didn't seem to help.

A few specific questions: What is the function of the O ring on the bottom of the main nozzle? The manual says "Critical" that it is in good shape. Mine is new but I've had the carb open a bunch of times messing with the bowl gasket and I'm not sure that has caused it to wear or improperly seal.  Second, is this more of a symptom of excess oil in the system? Like the crank seal leaking?

I feel like it was running pretty well after the initial carb rebuild but in the process of trying to get the bowl gasket to seal, this plug fouling problem has come up. I did swap back in most of my original Mikuni Jets as the rebuild kit I has didn't use genuine Mikuni jets and from reading on here the off brand jets can be way out of spec.

-Mike

If you can feel pressure pushing the bowl on then chances are the Oring is sealing ok. Does it just need a "damn good thrashing" to clear it out. Or is the exhaust restricted in the spark arrestor fitting deep in the end section. Float level ok--not dripping out the breather/overflow in the bowl. Side main jet fitting should seal pretty easily with fiber or alloy washer unless there's a problem there somewhere. Sorry not much help an i. Fit a hot plug & run it up for a bit until motor is hot then go back to your B8. I often use an old plug out of my 'old' car which is a champion N12Y & doesn't oil up or give up. I guess right side crank seal is 'possible' but unlikely as are a bullet proof seal on the early 250/360 motors up to "73. Also if that right seal was blown it would be very lean & gaspy & hollow feeling to the throttle--not responding instant as you twist it.

As far as the exhaust goes, I had that off a few weeks ago. There is is oil in it and the O ring from the expansion chamber is gone. There is also some metallic ring loose in the expansion part that I can't get out an have no idea how it got there. I'm assuming it was originally built inside the chamber itself because it is too big to come out either end of the pipe. The spark arrestor has been gone for a long time.

The o ring is quite tight when installing the bowl and visually looks to be ok, maybe a tiny score on one side but no tearing.

Floats are good as far as I can tell. The carb never leaked out of the overflow opening but the bowl gasket was weeping a bit at first, that has since stopped. I think the rubber gasket swelled and seated properly finally.

What kind of air filter are you using
Doug

New Genuine Yamaha air filter.

Try it with no air filter.  These bikes do not like the new sticky oil filter oil.
Doug

That part rattling in the pipe can be blocking exhaust flow.  I've had it happen.

at sea level my stock dt 360 was rich on the top end with the stock air filter and stock muffler baffle in. I was a little confused as to why but then I just dropped the main jet down to a 170 and stopped thinking about it!
a 160 main might even work on my bike. 
Jet your bike for what it wants.

I'll try it with the filter off, maybe also try getting a bit more of that oil out of the new filter. The ring stuck in the exhaust will be tricky, I'm not sure how I'll get that out since it can't seem to clear the bends on the front of the pipe. I'll give it a shot and report back!