[HIPPO]

4th slot from the top or the bottom, ie is the clip closer to the top or the tip of the needle? third groove being the center groove. Where are the three little washers?

Sounds unusual, mainly because the jetting sounds like it is quite rich.

 

[HIPPO]

The stock low jet used to be a 42 in 99 and then they went to a 45 stock.

Are you sure the low is now a 42 again?

If all the other stuff, ie intake leaks etc, checks out it may well be the bike is running so rich it is getting loaded up with carbon. These days if you see any color on the plugs you are too rich.

Try to run the thing with the needle either in the center groove or put the needle in the second groove from the top with one of the little washers under the clip effectively running it between the 2nd and 3rd groove from the top. Try a 175 main and a 45 low. Make sure the accelerator pump is working properly and spraying into the center of the throat.

Try running some strong cleaner thru it, like Techroline or Berryman's B12 and beat the $hit out of it for a couple of days. Maybe it helps.

If you want to see if the thing is carboned up or not you can take the pipes off and turn the engine over until the exhaust valves open. Then you can look in there with a flashlite and get an idea.