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I replaced all of transmission bearings on 75 RD  last winter. Ordered from "Yamaha Parts Online" (babbitts) and the prices were very  reasonable $218 bucks for all of them, all OE.

Check you front sprocket too.  I had a similar problem and it turned out the splines were not in the center of the front sprocket.

  

Check your timing between cylinders my guest is the right side is more advanced than the left.  I had a similar problem years ago and it turned out to be the timing was not synchronized between cylinders.  The specs are pretty liberal on this but I have found the closer you can get them to be timed exactly the same the better it will run and less likely to foul a plug.  That said the point plates like to move as you tighten them down so it can take some time to get it just right. Set your left side timing and the match the right side to it as closely as you can get it.  Just my 

I used a small dead blow hammer and gently tapped them in on mine.  Probably not the best way but it worked.

Is your pressure plate clocked correctly?  If its like the later 350s the pressure plate needs to be clocked correctly to get the clutch to fully engage.

You really need to add the air to get a good burn going  , it sort of sounds like the roar of a jet engine once get a good flame front going inside.

[A LOT]

I am sure some may disagree with this process but I cleaned my TE pipes with a torch and air compressor.  Start at the front and heat the pipe until it starts smoking then add air from the compressor (a leaf blower or the exhaust of a shop vac would probably work too).  Once you have the the carbon inside burning the outside of the pipe will glow and show the flame front moving down the pipe.  It will smoke A LOT as all of the crud gets burned out of the pipe.  Once the flame burns out the left over ash will just fall out.  The only draw back is that its unbelievable on how much smoke it creates, so if you have fussy neighbors it might not be an option.   

It looks like they bugger welded the tips back on.  The tips should be held on by a stud that goes through the center.  The studs have a tendency to twist off when you try to remove the nut holding on the tip.

   Sounds like its tuned spot on...

   Looking good.  What air filter and jetting are you using with the Millennium chambers?

Take your time when setting the ignition timing the point plates tend to move quite a bit when you tighten them down.

I a use bottle/paint can opener for disassembling gauges. Use vice grips to crimp the rim, once you get the right clamping distance set its fairly easy.  Make second pass set the final crimp pressure.

I also thought about there being a vacuum leak and will check it out to be safe.  That said when I pulled the plugs to check the timing I am definitely running rich somewhere, I am assuming on the bottom end.  At this point since I have made a lot of changes I am going to plug off the manifolds and go back to a known tune and work from there.  To many changes at one time just confuses things.  Once I get it all lined out with out the crossover tube I'll start over and change the pilot to a 30 and up the main to 185 or 190 and see what happens.  Thanks for the advice guys.

Thanks Mark.  I think I will block the holes and make sure everything is running correctly and then put the crossover back in and see what happens.  I had the motor apart this winter to change out the bearings and seals so I need to go back and check the timing too.  I didn't mess with the carbs but a dip in the sonic cleaner to make sure everything is nice and clean won't hurt. 

I probably need to find a technical paper that out lines the theory of how the crossover tube works and how the carburetor tuning is changed.