Thanks Mark, that's a good idea about the tape.  As for me only giving it a small amount of throttle I was worried of hurting something.  I may not know a lot about two stroke motors but I know that if a 4 stroke is pinging (and I'm not saying my motor was pinging), that you don't give it more throttle, that would be a bad thing!  I will give that a go in another video.
 

Might be going against what others have said, but I think it is running too rich - you say you are running a larger carb, how did you arrive at the jetting sizes, needle position and slide number?

Over the years I have had a number of different 2 strokes, and it really does sound to me like it is over rich - try dropping the needle a notch.

My Kawa Triple does exactly what your bike is doing if the needles are set too high - is the air filter clean and free flowing, and have you pulled the plug after a run to try and gauge whether it is running rich or weak.

Just my thoughts on the subject.

Good morning Andy, thanks for the reply and thoughts.  I arrived at the jetting by trial and error, first it was just the main jet but running fine everywhere else but then when I got the main close to the point where it wasn't breaking up at past 3/4 throttle it decided to start doing this.  I probably should have taken notes when jetting since I'm racking my little brain about the steps I took and when it changed.  Gonna try a couple different things this morning and take another video...

Tony - yes you are right about making notes, I have had this problem in the past when messing around with carburation, always best to make a note of every little change no matter how small.

Here is a link to the Kawasaki Triples website about tuning carbs - you might find it helpful, you will get there in the end.

Ok to the Triples have 3 carbs, but the basics are the same..........www.3cyl.com/mraxl/manuals/carbtune/carbtune.htm

 

Thank you Andy!

Ok, not sure if I'm still on the right story but just listened to the first video in post one with the headphones on & my take on it is that its an electrical issue. I know its at the same revs every time but still stand by that. It idles very retarded sounding although could be wild porting making it sound that way if its been ported. But ok if just plain retarded it'll be due to zero or almost zero points gap. So if you're using the original points mag--go looking at the gap & see if there's almost none. If ya running a model aftermarket cdi mag then I don't know--must be wrong again haha.
Close the plug to 20 too, just because.

Good morning RT325 (well it's morning here ), electrical has been in the back of my mind too.  I'm not sure how to set the point gap without screwing up the timing.  Setting the plug gap to 20 is an easy do, I'll give that a shot. 

Ok, & good evening, well it 12.55am so good morning too, but sleep time for me. Just thinking if it 'is' almost closed on points gap the the timing is miles retarded anyway. Just eyeball the gap by moving the flywheel forward & back about two inches over the points breaking area & see if gap looks about 15 thou max. If barely visible then open them up to tight 15. If it's an original mag then timing will be close. Just trying to prove a point & get it running right. Fine points of timing can come later if necessary. I could be way wrong with my diagnosis. Check your left main for any up & down by lifting the flywheel while you're at it. Night.

RT325 - Good shout, never crossed my mind, as the old saying goes, most carburettor problems are electrical !!

Here's an update guys, so I tried putting/leaving the choke on and that cleared up the part throttle issue so I put in a #20 pilot and that seemed good now it breaks up at 3/4 to full throttle where as it was running fine with the same main jet prior to me putting in the smaller pilot jet, which was a 15, hope that all makes sense. 

The issue I had with the pilot jet and is why I changed it from 20 to 15 is I watched MikuniOz's video on tuning Mikuni carbs and with the 20 pilot jet I could turn the air jet all the way out, or darn close to it without any change.  According to MikuniOz that means that the pilot jet is too big, so I went smaller. 

So, back to the 3/4 to full throttle breaking up.  Like I said it was running fine with the 200 main jet I had in it till I messed with the pilot jet so do I go smaller or bigger?  I have a 180 and 160 main to test if needed but if I need to go bigger I will have to wait until Tuesday to get one from the Yamaha shop.

As always thanks for the help!

EDIT:  One more thing (isn't there always one more thing ), with the air jet at 1 1/2 or even 1 1/4 out I have to darn near screw the idle screw all the way in to get it to idle at about 1350 RPM...