I have a 2004 zx10r that has 6k miles on it. It has a muzzys exhaust, k&n air filter, and a power commander. The bike gets super hot when riding at low speeds or when you stop. Within about 1 minute of stopping the temp light flashes and it reads about 240 degrees. I talked to Dynojet and they told me to re download the program which I did and reinstalled it using my laptop. The bike runs pretty good. The other day I was on the interstate with my brother who has a 1998 zx9r with a muzzys exhaust and a jet kit. We were running about 80 mph and we both dropped to 4 th gear. My brother signalled and we floored our bikes. His zx9r jumped in front and my bike stayed off his back wheel and could not catch his. I know the zx10r should smoke an older 900. Both bikes have stock gearing. Could there be something wrong with my exhaust valve on the header? I pulled the thermostat out of the bike and it is still getting hot.

 

Hey, watch out for those early 9's; they run better than you think.
Seriously, it sounds like your engine is running lean at low rpm. However, i would first check to make sure there are no obstructions, etc. in your cooling path. If your radiator is gunked, it won't flow as it should. (and in the OEM rads, that doesn't take much.) BTW, put your thermostat back in; it's there to do a job. I would also seriously consider the possibility of a blown head gasket. I have a 9 that was doing the exact same thing. I checked everything; even replaced the rad (with the custom job--see my gallery.) Turns out it was a blown head gasket (between the inner 2 cylinders; couldn't see it/tell from the outside and nothing in the oil!!)
It's not a horrible job to replace, but a little time consuming.
Just check all the "cheap" stuff first, before you take the plunge on the gasket. May not be the P-commander at all.
I feel your pain.

 

^ good info.

 

I have the thermostat back in. I only took it out to see if maybe it was sticking. The radiator is clean as a whistle and I am getting good flow through it. I haven't thought of the head gasket because it is not using up water and it is not smoking at all. I was told from a buddy that when I shift between first second then third a tiny blue flame comes out of my exhaust pipe. I think it is running lean on the low end myself. That is why I am leaning towards a problem with the exhaust valve not opening and closing properly. I have no idea how to check that though.

 

I would think that you may be running abit rich for your timing if flames are shooting out the pipes.

 

Have you checked to see if your cooling fan kicks on?

 

The fan does kick on. When I bought the bike the stock fan was melted around the edges. I replaced it with a Muzzys aluminum fan.

 

On the Muzzy fans, just make sure the leading edges don't "cut" into your radiator. I trimmed mine just a bit to give an extra 1/4" for the bumps. (This was back when I was running a rad fan/stock.) There's not much wiggle room between the fan and the rad.
You may want to see what your plugs look like...
Abad head gasket will cause your coolant reservoir to build up pressure and "puke." FYI

 

The coolant resevoir has run dry twice now. I broke down today and started taking the bike apart to check the spark plugs in hopes of finding one that was bad. If you haven't pulled the plugs on a 04 zx10r, then you don't know what you are missing. It took what seemed like 6 days to get them out. The middle two come right out, but #1 and #4 require you to take the motor mounts off of both sides which require removal of 6 bolts per side. All 4 plugs looked just fine. The ceramic part of the plug was a medium brown color. I have an appointment with the local dealer to do a compression check on all 4 cylinders this friday. I will post the results when I get them. If it is a blown head gasket, it should show up with a compression test.

 

resevoir running dry twice. Not good
lol on the plugs. Had to look in my manual to understand that one.
Yup, definitely let us know on the outcome