I have tested the fuel pump flow and found that it pumps less than the specified 6.4oz/10 seconds with 12v power supply. IIRC it was pumping somewhere between 5.6-5.9oz. to make sure we ran the test correct we did it several times. We also tested it for 20 seconds since any error in a shorter test will have a bigger effect.
Is there any possibility that what is causing the bike to not idle higher while in the "warm up" phase could also cause these problems?
Background Information of bike and riding habits
I will do my best to give the most information about bike and what kind of riding I do. My bike is a 2004 CBR 600RR. It has 37,xxx miles on the odometer, however I am not sure if that number is correct or not as the previous owner never told me if he ran a different sized sprocket. I am also not sure of how many owners the bike had before him. He only told me he laid it down on the right side, but damage to the fairings makes it obvious it has been down on both sides. While test riding the bike I noticed no strange noises or sounds and it ran just fine as far as I could tell. Ill admit I should have looked for common problems and things to look for on this specific bike before hand as something easily could have slipped through my radar. I did not notice any leaks in the garage where it was kept or in the driveway. I did not idle erratically, or hesitate at low RPM. I do not "abuse" the bike (no stunting, track, or extended periods of riding hard). I do open it up occasionally. More precisely I pull from 5-6k RPM in 2nd gear to 10-11k RPM in 3rd gear. My daily commute is mainly in city traffic (midwest) which isn't bad at all. Longest I find myself sitting still is 2-3 minutes id say. I tend to cruise around 5-7k RPM.
I first noticed the bike would idle a little rough, and would hesitate while pulling off from a stop when leaving school one day. I know 'rough idle' is too generic of a term so here is my best description. While sitting still at a stop light or any other scenario it will idle at 1500 RPM and depending on the severity it will drop from 1500 to maybe 1200 and fluctuate. Sometimes it will be very rough and will only idle like that, and other times it will be less severe and idle fine and hiccup every 5-15 seconds. Eventually it got so bad it would stall while idling or coming to a stop. I changed the spark plugs and it seemed to run MUCH better, however it will sometimes still idle and fluctuate just as much. ALSO I have noticed it seems to idle perfectly fine when the bike has reached over 200 degrees Fahrenheit (or else id have some more severe problems). For example if I get stopped in traffic and the bike goes above 200 degrees, the bike eventually idles at a smooth 1500 RPM and the hesitation while taking off is no longer present. ( if bike temperature reaches higher than 200 degrees it seems to idle smooth at 1500 and no longer hesitates at take off and does not return for the duration of the ride)While idling rough at a stop light I believe it makes a "knocking" sound (while idling if your snap the throttle back it will slightly hesitate at lower RPM around 3k and rev normal past that point)
Possible related symptoms?
prior to changing the spark plugs the bike would stall while turning right. ( this was when i noticed it was no longer safe to ride IMO)
When idling rough at a stop it will sometimes make a knocking sound. I never noticed this prior to changing spark plugs
while turning left or right from a stop i can here a clunking noise.
I have noticed the bike idles at the same RPM regardless of whether the bike is cold or warmed up
The old spark plugs were black/brown and were the exact model the service manual recommends. The new ones are the same model NGK as well (they were not oily when i changed them but the bike sat for 2+ days while I waited for new ones)
The ignition coils are not cracked or melted and the connections are not corroded.
The ignition coils ARE easy to twist by hand, but not so easy that they can freely spin. I read in a spark plug DIY guide that they shouldnt be easily twisted so im torn whether or not mine are too loose. also found it weird the tops were threaded.
After changing the spark plugs I started up the bike and it idled smooth at 1500 for 20-30 seconds. ( i did not warm it up to operating temperature since the radiator and etc. were resting below their mounts (the cooling system wasnt opened though, i just unbolted the radiator and nudged it down to make for a little room.) i assembled everything and started it up and it idled okay for 5-10 seconds and started to idle roughly again, although it stayed running until i shut it off. I stripped it down again so i had access to the coils. i will label the coils 1-4 starting on the left side when you are sitting on the bike
I first started up the bike and it idled rough. i removed all the spark plugs and none were dirty. upon putting them back in and connecting all the coils i started it up again and it idled and revved fine. i took it for a casual spin around the neighborhood and it was fine for the first half however i noticed it started to have a slight "lump" at idle but would take off with no hesitation. After opening it up down a stretch of road (and catching a crazy look by a fellow rider on a Harley, though to be fair I was riding a bike missing all the mid-lower fairings on left and right side along with no gas tank cover) i returned home to the bike idling at a relative steady 1500 and revving perfect IMO. I rode it to class the night and after class it idled rough on startup and i had the genius idea to turn the idle up to 2000 "since when the bike is cold it is supposed to idle high" I KNOW that was stupid for a few reasons. 1.) the bike will idle higher naturally based on the temperature due to the wax unit (correct?) and 2.) idle is supposed to be adjusted at operating temp which i believe is 180f, and idle is supposed to be 1300 +/- 100 RPM. This is all the time I have to explain for now im sure i will update it regularly with new information and findings. I appreciate any help i can get. I also realize the bike has many problems and im sure it is not just one thing. BTW i am a novice at mechanic work. i can perform most basic tasks like coolant flushes and general part replacement. I have more information to update but i am busy ATM. When I find time i will upload videos of the bike as it will be easier to hear than to explain. if anything requires clarification just ask ill be happy to explain! Thanks for any help or advice. Happy Riding!