motojoe

Does it have a carburetor or is it fuel injected?

Your engine is still running lean! Adjust the air/fuel screw and if you can't get it to run better then take off the top of the carburetor and adjust the needle by setting the "C" clip one slot further down to get a richer fuel mixture.

On the top of the carburetor take off the two or three screws and remove the needle and adjust the "C" clip move it down one position and test to see if that helps. As well adjust the fuel\air adjustment screw that is either on the front or the rear of the carburetor. When the engine is running (idle) adjust the screw until the engine starts to speed up then adjust the idle screw until the engine Idles at the speed that you want.

Also, those Kawasaki Mules that have the two cylinder engines are subject to their push rod bending, that also could cause the engine not to start and or running poorly.

replace your pickup coil (sometimes it is called the crankshaft sensor) and check your battery connections

Check to make sure all your hoses are connected to the throttle body.

It appears that if it is still smoking that your new head gasket is leaking. It happens!

Check your crankcase oil level, if it is too full then that means that your carburetor is leaking fuel into the engine when it is not running. Your carburetor is overflowing to fix that adjust your needle and seat so that the fuel flow stops when the carburetor bowl is full. The reason for gas being in the carburetor air box is that the crankcase breather is trying to re-leave pressure because the crankcase too full (gas and oil). Fix the carburetor problem and then change the oil.

Yes I would replace the flywheel if the magnet is no longer there. The pick-up coil on the stator when the magnet on the flywheel pass it give out a electric pulse and also determines the engine timing the ecu if there an issue with the timing then I would check the key way on the flywheel. Second I would check the camshaft timing to flywheel to determine that your valve timing is correct.

You probably need to replace the ecu since the stator give a spark pulse and the ecu is not connecting to the ignition system.

If you already replaced the stator and the pickup coil make sure that all your connection are connected. Crank it over by the starter motor and hook up the wires from the stator to your test meter to determine if power is coming out of the stator, then check the coil to determine if your are getting power.

On your picture I see camshaft gear and marks but on the head there should be marks to time the camshaft to. Unless that grease mark on the top of the picture is a timing mark your are out of time by at least 40 degrees. Find the timing marks on the head and line up the camshaft timing marks.

Sounds like you have an air bubble in the cooling system. What you need to do is jack up the front of the side by side with the wheels off the ground and bleed the system and fill the radiator.,

Just look on your original starter motor for a manufacture's name or a part number, then look up the part number on google and buy it from any of the vendors that come up BMS is usually way over priced. I have a ranch pony and have really good luck with it but most of the parts from Chinese side by sides use the same parts.

Need more information: Do you have spark? Is your fuel pump working? Is your starter working?

It appears that your stator pick up coil is going bad

When filling the radiator to bleed the system make sure that the front of the vehicle is jacked up higher that the engine to get the air out. Sounds like you still have a air bubble.

your brake switch is bad.

Check your connections and it is probably your starter solenoid.

Take your thermostat out, it may not be working also bleed the system as you may have air cooling system.

Check your thermostat, make sure that it is not stuck, to check put it into hot water to see if it opens.

It appears that there is something wrong with either the carburetor or the fuel injection. If it is carburetor engine then the needle and seat is not sealing or your fuel pump is staying on. If it is fuel injected then your fuel pump is staying on when the engine is off. Either way make sure that your fuel pressure is fixed before you run the new engine or it will fail again.

Look at the "Man Hole" threads and you will find a cut into the threads, line this up to the flywheel timing marks and that will be your TDC.

Just for fun if your compression is as low as you say check the valve adjustments a tight valve could cause the loss of compression and also cause it not to start.

Replace your stator and it should come with a pickup coil. that should fix your problem.