Staff SGT

I am new here and I am try to get my WC working. If you can give some insight, it would be great. I was given a 2001 Kawasaki stx 1100 DI with twenty three hours on the machine for free from a friend. The ski sat under a tree for three years and it was full of gas. My friend said "you get it running and it's yours". I work on eight million dollar Blackhawks for the US Army, How hard could it be? I started by draining 14.4 gals of bad gas, then dipping the fuel pump, then replacing the fuel filter, new plugs, fresh gas, and then dipping injector tips. The fuel pump is at 21 to 25 psi (with in range). The machine started and it blew a lot of grey smoke but it cleared up after three mintues with water running. I took it for a test run and it got up on plane at 10 mph and then the machine went into limb mode. I got the machine home but the machine runs rough and there is no throttle response. Now I am lost. Do I have to get the computer code(s) wipe off before the machine can work correctly again? Kawasaki is upseting me the way they treat thier costumer. Thank you for your time into this matter.