What is the part number on the spark plug to the left in the pics, the plug with the blue coloring?

NGK DPR9EVX Blue bands..

Is that the original OEM plug? Have they been changed because you have mixed plugs?

I have had issues with nylon tubing when used as a vacuum line before. Not sure if it is contributing to your problem here. When the vinyl heats up, it becomes very soft and will deform, which COULD cause a vacuum leak

That clear vinyl tube in the pics is attached to the PAIR control port on the front carb. You are correct to have it plugged on the end, though it would be better to use a vacuum cap right on the port and eliminate the possibility of fuel getting trapped.

Clean the spark plugs, drain the fuel from that line and try running it again. You might want to shorten that clear line and have it run upward to prevent fuel from getting into it again.

Are you still running the K&N air filter? When the bike tipped over, did any gasoline get into the air filter?

Ladies and gentlemen, I have concluded this chapter, After a month of learning new cuss words in a variety of different languages, slamming my head angst the floor numerous times and spending countless hours NOT knowing what to do next…… she is all better  please allow me to explain..
After falling over in my garage she had a sputter and choke out symptoms at 4000 Rpm.
Since discovering this problem I have torn apart those carbs two dozen times, replaced choke holder guides, jets, gaskets, diaphragms, replaced and upgraded the coil system to the 600RR coil pack, replaced every vacuum line, PVLIR and fuel lines, rewired the R/R .. then today discovered that I “may” have an ignition amplifier failure… after all this plus new plugs and replacing the Ignition amp she fired right up.. took her out for an hour ride, she sputtered a little bit probably due to needing a carb syncing. But thank you to everyone who offered words of wisdom.. thank you very much
Josh

In case no one has told you those plugs are way rich and the gap appears huge and the proper plug is NGK DPR9EIX-9. It is Iridium tipped and available on the Internet for @$7ea.

or can go to the auto part store and get them,thats where i get them and they are the same price.

You're absolutely right, I bought mine at O'Reilly auto parts. I drew a mental blank when I was typing this morning.