Mikuni main and pilot jets are calibrated with fuel flow numbers (in cc's a minute I think) under specific calibration conditions. 

Higher number flows more fuel so is a richer jet.

The nice thing is short test rides won't hurt a thing, and if you're dialed in to where the problem is you're going to instantly know if you're making an improvement or not. Don't stress the test rides, it's the long term rides where incorrect settings set up for failure. Testing based on your knowledge of the problem area probably takes super little time to find, and your result will be somewhat immediate. You have the clues from other members, just get the different size jets, leave your tools out, and spend a couple hours swapping jets, get closer to where it doesn't break up, and then fine tune the needle. Nothing wrong with large jet changes to force "change" as long as your ride isn't 20 miles. 

Just my idea, but go up to 220 & you'll know straight away if it kills the top end & blubbers--so is over-rich. If that happens then go down to a 180 & once again you'll know straight away with a 100 yard dash down the road. At 180 you're still above what you say is original std size so should be plenty safe. But first test by going up in size as can't do any engine harm that way.

Thank you to everyone, I ran into a small issue when looking at jets.  The common kits go up to 200 or start at 200 (which is where I’m at now).  So I pulled the plug and it is black (it was brand new).  So that helped me decide that I need to go to a smaller jet.  I’ll get them in a few days and I’ll report my findings after I get some time to play around more.  I am glad it was running rich, I drove around for a while playing with the screws on the outside of the carb before I posted this and am glad that I most likely didn’t damage anything running it rich.

Update,  I finally had time to work on my bike and after a series of swaps I’m down to 160 in jet size which is the same jet as the original.  For the most part in gears 1,2 and 3 I have very smooth running all the way up into high rpms.  In 4 and 5 though I get sputtering and missing at high rpms.  I also have a top speed of about 50, which I think is a bit low (remember going 60 on this bike with no problem).  I don’t know if I should go any lower with the jets as the smoke has all but disappeared and I don’t plan on riding this thing fast at all.  Mostly for going to work in town.  

so my question is, other than carbon build up am I doing any harm if the jet is a bit on the rich side?  Also it was super hot 99F but low humidity yesterday, am thinking I should try on a cooler morning to see if the same thing happens.  Getting so close, just don’t want to wreck anything now!

Looking back a page i see i mentioned exhaust in the middle of talking jetting so copied the relevant bit below just to keep it in mind.

Or if the exhaust is strangling it through carbon buildup in the muffler which if bad enough will give rich full throttle symptoms.

If anything I have the opposite problem.  When I put my new tires on the back one was slightly larger and I had to take the muffler off to get it to fit without rubbing.  Now it’s sort of just hanging loose, the exhaust goes through it, but some leaks out the sides.  Could that be my issue?  Early on in the higher number jets I could see the smoke heavy at full throttle now it’s really not noticeable, so my gut tells me I’m close.  Next time I get some time I’m going to look at the plug to see if the blackness has changed from my earlier runs