Check your manual for a description of the auto choke. See first of all if it remains in place and hooked up, based on what you find in the manual. The auto choke depends on a properly working cooling system, so will want to make sure the impeller and t.stat works -- need to be in a test barrel or in the lake to test.
There is a manual override for the choke -- believe it is on the right side of the carb, looking at it from the front. The choke may not be fully opening, giving rough running at idle and difficulty dialing in the low speed mix. After it warms up a little, I would use the manual override to turn off the auto choke, then try again to set the idle mix. When finished, changing back to the auto choke setting should not affect operation (i.e., the choke should remain open).
But first make sure the cooling system works -- need a strong water spray out of the exhaust port on the leg. Head surface temp. should be about 140F (not too hot to touch).