Backfiring

Yes I believe so as it is also throwing Flame! The exhaust does not smell rich, if anything it smells a little lean. So I thought I'd post on here get all the ideas while I've got it taken back apart try to cover them all. my first Kawasaki and I've never had one to revive that has set this long.

THAT could also be a couple of cylinders not firing and raw fuel going in to the exhaust and then getting ignited by  the exhaust coming from a fired cylinder. So if that's the case, a fresh set of sparkplugs may be in order. You could confirm this by checking the temperature of the down pipes while warming the bike up. Cold pipes- dead cylinders
Backfiring is a confusing term. Most mechanics understand the term to mean firing back through the intake/carburetor or throttle body. 
Misfiring- Is generally understood to mean explosions from the exhaust. So I guess we should have confirmed just "what" was going on before throwing out ideas.
 

Changed the plugs last week. The temps on pipes were about 150 on cylinders 1 and 6 the rest were about 250 to 280.

So I bought an injector cleaning tool, and the injectors for cylinder 1 and 6 are completely stuck burned up 4 resistors trying to get them to open! Any ideas on where I can get 2 injectors? Or a way to free them up?

Try soaking them in Lacquer Thinner for a couple of days. Works amazing for cleaning up the carbs with varnished inner passages. Since joining this site and reading Scotch's carb cleaning methods primarily with Lacquer Thinner, I've been using it for all sorts of cleaning. I now buy it by the gallon. ( Thanks Scotch)

Ok took the resistor out of the power wire going to the cleaning tool and hit the power in tiny burst and they are open and spraying a nice clean mist! Will finish reassembly tomorrow and see what happens. Thanks again for great ideas......fingers crossed.

If you need FI work, Russ Collins Engineering does really really good work.