My Miikuni is running REALLY lean. Do you guys recommended putting a bigger Jet in or adjusting the needle setting. I have a 2.3 jet in it now. (Head work has been done etc...)

2.3 refers to the needle and seat combo and has nothing to do with rich/lean. Check your main jet for size and that its clean with no geen stuff groing on it. Better list your engine and your mods .we can point you in the right direction on correct jetting

Thanks Will, I have had the heads decked down .50 running a stock non gutted can right now. (gonna try to find a happy median with noise and power this summer) have an 08 PD non CDI. I soaked plugs and had to change them at the ramp a couple times this year at start up. I noticed she was running really lean prior to putting the new can on it. Im up north and hunted in sub zero temps this year. the motor would idle but when I engaged the clutch i had to pull out the choke to give it some fuel to keep running.

Soaked the plugs? Plugs don't tend to go bad with a lean condition as quickly as they do when running rich.

It flooded after start up, so I had to switch out the plugs. Then after fought with the throttle to keep it going and she warmed up it would idle fine, but when I engaged the clutch if I didnt pull the choke out it would die.

Aside from your random flooding sounds like your idle might need might need a little more fuel. Have you adjusted your idle air screw yet? As far as wide open fuel running lean you should check the main jet size. It may be a 160 and you might need a 170/175 with that low of a temp up there