Great suggestion.  I will try that.  I also have the old coils it came with I can put back on.  I was originally fighting ignition issues and thought a better spark would help and replacement parts are limited!

Economy Cycle in Texas should have brand new OEM quality coils. Use code "2SW' for a discount (if code still works, has for years.)

Sorry if I am replying all, I was intending to respond to each comment. These are all fantastic suggestions. I have lived many of these gotchas. The battery is key. I think I want a volt meter on the instrument cluster! I have installed the bowls on the wrong side before! I have certainly missed the step of connecting the tube between the carbs! I think I am going to try the timing light. Also, jumper cable to my lawnmower 12V battery to see if anything changes when it's failing. I will revisit the carb sync. I'm with all of you on the pain of taking the carbs on and off and messing with the points!! I wish Yamaha had put a bowl drain screw on these. One other thing I though of is the 0.25 over bore and new forged pistons might have changed the compression ratio (even though they were not supposed to). What do you all think on the stock jet settings? Should I be expecting more fuel mixture? The K&N replacement element in the original air-box I would not expect to change as much as I am seeing. Thanks again!

If possible please a good long video of it running helps to diagnose problems a lot easier.

Ok, everyone I found the primary issue in the carbs. Special thanks to @RT325 for suggesting the throttle slides, which were indeed in the wrong carbs causing excessive richness low to mid. The cutaways now face the inlets and it runs completely better. Now I have fading in the power band under load, so I am going to move the needle clips down before I re-jet richer. Wow, what a difference. Hard to hold onto her when she takes off!

Oh cool, i'll sleep well tonight haha.
Yes sounds a bit lean-ish now from what you say.
Sorry if i kept harping back to the slide theory but we got there.
So choke interconnecting pipe is fitted on?
Just thinking from a leanness point of view but it'd be more than lean if the pipe was off from either end--which would affect right side only as left side controls the choke so when choke control is shut off no extra air would get to the left side.
If that make sense--its late here lol

Yes, the pipe is in place and the bowls are right.  I'm at 125/30 jetting with the c-clip 3 down from the top on the needle.  The bike was with 120/30 needle 4 stock, however the idle is slightly rich at 1.5 turns out on the air screw already at 30.  Next time I'm in the garage, I'll check the plugs too.  Thanks again.

I guess we've mentioned exhaust baffles from a performance point of view.
Thinking back, they were quite restrictive with a quite a small pipe at the outlet end which means they catch lumps & stuff if there's bits bouncing around in the main muffler & get lodged in there.
Mind you they have to get through the rest of the baffle first & can build up anywhere through there.
Maybe different markets had different baffles, not sure.