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The sound you hear is caused by the expansion and contraction of the metal caused by the heating and cooling.

It is more prevalent in an air cooled engine because there is more heat generated. That is why air cooled engines make so much more noise when first started when cold (piston slap).

Air cooling is simply not as efficient as water cooling. There must be looser tolerances engineered into the engine to allow to the extra expansion that takes place.

Water in gas or timing is off. Change the spark plug and check the carb bowl for water. If there is, then drain the tank and clean the carb.

Additional comment:

Often when you have a motorcycle or ATV that is backfiring, you will find that your bike is having a problem with bad spark timing. This will also cause your jerking...

Take your bike to a professional and have them look at the carburetor adjustment and the timing.

There are several answers to this question.

Answer:

Sounds like you have stuck floats in the carbs, or carb. May have some foreign material that got stuck in the needle valve holding it open causing the engine to flood. You can either remove them or take the bowl off and clean it. Then adjust floats if they need it. You can also run a little bit of Marvel Mystery Oil (available at Wal-Mart) through your next tank of gas to clean out tank and carbs. This won't hurt the bike.

Answer:

That previous answer is a little vague. Here's what you do: If you can take your carb off, you can most likely clean the carbs yourself. Go to your local auto parts store and get the carb cleaner that comes in a can that looks like a paint can. After you get the carb or carbs off the bike, carefully and slowly take the screws off the bottom. This is the float bowl. Be careful not to rip or stretch the gasket if there is one. You'll notice the float. Slide the pin out. Remove float and watch for the float needle. Note its position and where it fits into the carb. Now, you'll see a few brass fittings, some look like a flat screwdriver could take them off. Do it. Others might be a 6mm or 8mm wrench. Do those, too. More complex and modern carbs have more components. You may want to remove the tops of the carbs and take everything out, but this usually isn't necessary. Take all of the metal pieces you just removed (no Rubber) and drop them in the ChemDip carb cleaner as per the instructions. 30 minutes is good over night is better. If you're scared take your carb(s) to the bike shop and ask nicely if they'll slide your carb in on the side and clean it....ask and ye shall receive...

Answer:
 
In other words "How do I remove a flooded condition?"
A. Shut off your fuel valve.
B. Open your throttle slides/butterfly and keep them open, while;
C. engaging the starter, until;
D. your engine fires and starts.
E. Open the fuel valve.
This should remove the excess fuel condition. Be aware that the starter is not designed to be "layed on" for too long.
Remember to shut off your fuel valve after turning off your ignition circuit so as to avoid a future occurrence of this problem.

Answer:

Along with everything stated above, change your oil and run a quart or 2 through then change your oil again..I have a carb 4 wheeler that had the fuel left on for too long and the carb took in so much fuel that it actually started overflowing fuel directly into the engine. Ended up having more gas inside my engine than oil. I got lucky and drained it before I ran it. If I ran it, I probably would have a rebuilt engine right now.

The best article I've read on the web concerning 4-stroke engine break in, can be found here: http://www.mototuneusa.com/break_in_secrets.htm

Engine break in is very important, proper break in will help ensure long engine life.

One common reason for the gears sticking is incorrect oil type, motorcycles have wet clutch and specific motorcycle oil must be used, otherwise the clutch drags and gears are hard to shift. Aside from any major problems with the transmission itself, is your clutch working properly? Is it set correctly and fully disengaged when it is not being used. I would start here. You may need new plates in your clutch itself.