Need help to bike running at peak and other questions, issues

So, to summarize: I bought a used 03 xb9r with ~13k+ miles on it.
Condition when I bought it: bike was in good shape cosmetically, has run well since I got it and came with a Jardine. But I have no idea what has been done to the bike.
Condition now: Currently has 15,200+ miles on it. Oil changed to Amsoil and Mobil1 filter. Jardine has been replaced with stock pipe. Tuned suspension per the service manual to my weight, etc. It currently gets 38-45 mpg on average.
Known Problems:
1. When engaging the brake lever, sometimes it will stick and then all of a sudden engage. I've heard some say I need to disassemble and lube.
2. Sometimes when I come to a quick stop, then apply the throttle, I get a brief cutout or misfire. [confused]
3. So 2 weeks ago we had a torrential downpour and when riding home, one of the cylinders (the back one i think) was cutting out at low rpm. It almost made me wreck as i was taking a turn and gave it throttle and the 2nd cylinder all of a sudden kicked in a around 2.5k rpms. It hasn't happened since and makes me think a plug/wire/etc was getting grounded somehow from the water.
4. Also, (may or may not be an issue) if i hold the throttle constant at around 4-4.5k rpms, the bike seems to subtly buck a little.
5. Clutch seems "crunchy" at times. Should I change the primary oil to remedy this or is this just the nature of the buell tranny?

So, what should I do to get the bike running peak and solve these issues?
Would changing plugs and wires help, you think? What else should I do?

bump [confused]

changing plugs and wires sounds like it would help you a lot.

is the brake lever aftermarket or stock.

clutch should not be crunchy. lubing the cable might help. you should change the primary and engine oil anyway for piece of mind.

changing plugs and wires sounds like it would help you a lot.

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ok

is the brake lever aftermarket or stock.

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stock

clutch should not be crunchy.  lubing the cable might help.  you should change the primary and engine oil anyway for piece of mind.

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sorry, i meant shifter. like when i shift and it engages a different gear, the engagement feels crunchy

the shifting does kind of suck on these bikes so its hard to say if what you are feeling is normal or not. i dont think mine is that bad except 1st to 2nd. its not as easy to shift as many other bikes ive ridden thats for sure.

take the front brake lever off and see if you can figure out why its sticking. are you sure its the lever. maybe the caliper is frozen and the pistons dont move until there is a certain amount of pressure built up. good luck, the front brake issue should be addressed though. its kind of important

My bike seems to hesitate on low RPMs especially when cold. It's a symptom of running rich. Remapping the ECM and/or changing the O2 sensor will likely help as well as changing the spark plugs and wires.

My clutch cable snapped recently and I had to replace it. I realized when I got the new one installed how poorly it was adjusted. It seems like they're susceptible to break around 15k miles. Also running low on primary fluid will cause a crunchy shift. They do normally shift clunky though.

What's the word 28003?

haven't had a chance to really do anything yet except take off the brake level, clean it and hit it with some wd-40, and it seems to not be sticking anymore.
current status:
-idles low, sometimes acts like it doesn't want to start (but always does after a few tries), 38mpg regularly

i will change the primary oil this weekend. i am currently running mostly 94 octane, ethanol-free, sonoco gas (with a few times i had to use shell)

my plan over the next few weeks is to replace all the crap on the bike that's questionable, especially spark plugs and wires, and air filter. then, if that improves things, i will get an ECM cable and check out the mapping

Wow, 38 MPG seems really low! I get 45 MPG pretty easily. Does the exhaust smell like gas? When you're working on it, try at least cleaning the o2 sensor, see if that helps your idle/startup/fuel mileage.

Also reset the throttle position sensor. That seems to help some of the fuel related issues (bucking/hesitating).

where is the O2 sensor?

Rear Header pipe - Removal process with pics in the Service manual - Section 4.32 - You can download via link @ top of page.

changed spark plugs and wires. it seems i may have solved at least one problem

Rear plug:

front plug:


so i don't really see much difference with the way it runs.
Question: it was really hard to get the front plug on and i'm not positive if its all the way on. so would it throw an error, or CEL if it wasn't getting a good connection?

bump

Did you say it had a Jardine and you put a stock muffler on? From what I can see of the plugs it is running reall rich, does it have an inline tuner module/ Power Commander or some other brand, that is fooling the ECM to run rich, or o2 sensor may be bad, when they fail the ECM is supposed to go to max rich, let us know what you find

When you put the stock muffler back on did you make any changes to the ECM? When the Jardine was put on it may have been reflashed with a race map. Going back to the stock muffler would restrict the flow of air coming out of the motor and make the bike run rich, like Uly Luigi mentioned. You may need to reload the stock map for the bike depending on what other mods were done, if you have ECMSpy and a cable you can compare the two maps and see which one is loaded..

Did not mod the ECM. have no idea what map is on it.
i guess i need to get the cable and check it out asap.

1. will ECM Spy tell me if the O2 sensor is bad?
2. also, (previous question)

it was really hard to get the front plug on and i'm not 100% positive if its all the way on. so would it throw an error, or CEL if it wasn't getting a good connection?

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I'm not sure if ECMSpy can be used to test the sensor as I haven't done very much with it other than to load my race map and perform a TPS reset.. I have read all the warnings about running with a hi flow filter and an aftermarket exhaust without loading the race map because of how lean it would be, so that's why I was thinking you may be in the opposite situation now.
I know its tight when replacing the plugs as there is not much space in there. Depending on how tight it went in you "may" have cross threaded the plug hole. You definitely want to check for that and make sure it is in all the way or it could back out on you while running..
I'm kinda new to the Buells myself and my knowledge is sorta limited to my experiences but I'm sure someone else could touch base on those questions..

Just a guess, but, I would say yes, it should throw a code if the plug wire was not making contact, I think it would be a coil fault, make yourself 100% certain it is on, otherwise, it could become an intermittent problem, and a real booger to diagnose.
The O2 sensor would definitely throw a code.

Just a guess, but, I would say yes, it should throw a code if the plug wire was not making contact, I think it would be a coil fault, make yourself 100% certain it is on, otherwise, it could become an intermittent problem, and a real booger to diagnose.
The O2 sensor would definitely throw a code.

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ok, good to know. the dash is currently not showing the CEL light on

Moto: i didn't cross thread the plug, i am very careful about that. i was asking about the plug wires since i replaced them.

i will get the cable, clean the O2 sensor, and do a TPS reset and load the stock map on and see how it works out. i think the bike is running way rich as i'm getting about 38mpg consistently running 94 octane non-ethanol gas

Moto: i didn't cross thread the plug, i am very careful about that. i was asking about the plug wires since i replaced them.

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[up]

Ok, cool. I wasn't sure..