Okay so I finally went to get the bike started and it would not start, sprayed starter fluid and it started for a few seconds. Cleaned the carbs thoroughly and added a factory pro jet kit. The instruction to the kit stated that it needed 135 main jets for a K&N filter, so all 4 main jets are 135. I go to start, spray a little gas into the carbs and it fires right up. Well i let it run for a few minutes and I notice a white smoke coming from the engine itself. So i shut it off. Start it again and the same thing happens when i open the throttle wider. This goes on for a few times so that I can try to figure out the cause of the smoke. Now the bike will only start with a few sprays of gas and only stay on for a few seconds. Not sure if its the jetting issues, or there might be a deeper problem like a bad head gasket. Looking for any suggestions or help. Now I saw on a video that the 2 and 3 carbs run hotter then 1 and 4, so should all 4 be 135 or should I lower 1 and 4 and keep 2 and 3 at a higher level. I am new to jetting so please be patient with me.

 

I would think that its more important that the jetting is in the ballpark generally speaking, more so than the 2 inner cylinder being richer than the outer 2. I dont think your problem is because all 4 jets are the same. Motorcycles for years and years have had all 4 jets the same, and they ran fine, even the F2. White smoke is moisture from sitting or if it continues then that would indicate coolant leaking into the combustion chamber.

 

+1 on what CMF said. The white smoke is a bigger concern. Keep an eye on that. Incidentally, on the f3, with f3 carbs, carbs 1&4 have 135 mains 2&3 have 138. But not having that won't the issue you are describing.

 

Short Video in attachment of noise i am hearing. At this time of this video, I had the airbox off, only K&N on top of the open carb.

 

how much oil do you have in it?
That sounds internal and in the top end.

 

oil is full, that is what I was thinking also, definitely internal. It seems to go away when i open throttle.

 

Aside from the pecking sound, the idle doesn't sound good at all. It doesn't sound like all the cylinders are firing.
As a side note, a little over a year ago my Jeep started making a similar sound. I swore it was a lifter tapping. It did the same thing, peck on idle but go away when the engine was revved. I took it to a trusted mechanic who thought the same thing I did. Before he opened up the engine, he called a friend of his who worked at as a mechanic at a Jeep dealership. In about 5 seconds the guy told my mechanic what the issue was. He said the year Jeep I have is known to have their crankshaft bearings go out. He confirmed that it sounds like the top end, but it isn't. So that is what was changed and he was spot on correct. The bearings are what was making the noise.
I don't know if any of that is applicable to your situation, just thought I'd share.

 

How much work is this to tear into the engine. OR should this be left in the hands of a trained mechanic. I am only $400 into the engine, would it be better to look for a replacement and save myself a headache. I mean I assume I gotta get all new gaskets, etc, etc, etc.

 

It all depends on how mechanically inclined you are. Also how full is your toolbox? Finally, what is your ratio of free time to money? Tearing into an engine isn't a cake walk, but it is something that can be done.
Only you are the one that can answer that question for yourself.
Generally you can pick up another engine for fairly cheap.

 

Well I have a solid top end from a CBR600F2 which I hope will work for the F3, maybe if I can use that as a donor for parts, but if I do have to go deeper then the the top end, I think you are right, i might just go with a new engine. I think I will take it to a shop and get a diagnosis. I hear the f4i is worth the investment. No more carbs worry. I'll just have to take the hit on the bad F3. Thanks Alot