I'm writing this on my cell, so I apologize for typos and auto corrects, lol...
Ok, so its prob not fuel then, I wouldn't do anything else related to upgrades until you sort out the mechanical cause. All four stroke engines work exactly the same...
Suck- air/fuel charge is drawn into the cylinder...
Squeeze- charge is compressed...
Bang- ignition/power stroke....
Blow- exhaust is pushed out...
It sounds like the engine has dropped a cylinder(s). The easiest way to check this condition is to disconnect one plug wire at a time and see what happens to the idle. If this is the case, the idle will not change much, if at all, when the wire is removed from that cylinder. I'm going to assume that you have replaced the wires, if not, check the resistance with an ohm meter or switch two wires and plugs and see if the problem moves to the other cylinder with the wire and plug. If it does, replace the plugs, wires, cap and rotor.
There are several options at that point regarding further diagnosis, I prefer doing a cylinder leak-down test, although a compression test is effective as well. The difference being that you can pinpoint exactly where the compression loss is going.with the leak-down option. Most parts stores will rent or lend the testers.
The initial steps for both tests are the same, disable the ignition coil and pull all the plugs....
Compression test- starting with cyl #1, screw the appropriate adapter Jose into the spark plug hole until the o-ring seats, hand tight is sufficient. Crank the engine over for a few seconds, no more 5. Record the results from each cylinder, you should have about 150-ish PSI. If there is more than a 10% difference between cylinders, you found the culprit. The problem is that you still don't know what the cause is. If two adjacent cylinders are low, suspect a blown head gasket...
Leak-down test- You will need an air compressor for this one... Pull the valve cover, insert hose in plug hole, rotate the engine until the test cylinder is at Top Dead Center with the valves closed. Hook up your air supply to the tester, some of these have a regulator, adjust it untold the gauge reads "0" PSI. Connect the hose from the plug port to the tester, record the results. Up to 10-15% is ok in an older engine. Now, here's the cool part. When you isolate the cylinder with the highest leakage, track down where the compressed air is going...
Valve train-cracked head...
Adjacent cylinders- head gasket...
Tail pipe/intake- bent valve...
Radiator- head gasket/cracked head...
Oil return holes in the head- bad rings or scorred cylinder...
This should keep you busy for a bit, but its the only way to really figure this out