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My fj1100 is running rich. Low rpms are ok. Anything between 1500 and 2900 rpms in any gear runs like crap unless its being given less than 1/8 throttle. I'm thinking it might be the needle seats.
But the clips on the needles are all the way to the bottom of the needle . where should these be set there are 6 grooves?

So it is running rich in the mid range......................and you have aftermarket needles with 6 grooves.................and the clip is on the bottom grove (the richest setting)

hmmmmmm sounds like you need more air in the rear tire to me.  :pardon:

I blew through Reno on the way to the WCR and mine ran OK on position 4. If your bike is stock put her on 3 as a starting point. And I can say this enough, it is easy to get a vacuum leak in your diaphragms. Make sure each one is seated correctly and that the cap is flat where the screws go (RPM has some nice allen head screws). Hard to explain, I have seen them distorted because someone over twists on the screws. Lay the cap down on a flat surface with some 400 wet or dry and give them a rub while apart. And I am probably going to get slapped where it hurts when I say this but, I take a small amount of automatic transmission assembly lube (looks like clear Vaseline) and coat around the seal.
George

To my knowledge the bike is stock. And.  Only 23k on the clock. Is there supposeto be 2 washers on top of the C clip and do you mean 4th position from the top of the needle.right whoever tuned this old girl had no idea what they were doing

Forgot to mention I have k&n pods / 4 to one with supertrapp with no baffle plates on the tip

Quote from: stephenmcd on June 10, 2013, 08:33:35 PM
To my knowledge the bike is stock. And.  Only 23k on the clock. Is there supposeto be 2 washers on top of the C clip and do you mean 4th position from the top of the needle.right whoever tuned this old girl had no idea what they were doing

Yes 4th slot down from the top. The 3rd is a good starting point. One of those washers is about 1/2 step. Hope it helps your problem.
George

This is a good read http://www.fjowners.com/index.php?topic=658.0 (http://www.fjowners.com/index.php?topic=658.0)

OK thought I had it all straightened out with the carbs. Obviously I still have some issues. Now the bike will not idle when cold. I start with full choke till the idle drops. Then switch to half choke runs for a few minutes then dies like its running out of fuel. Any ideas fellas?

Idle should not drop on full choke.  In fact, it should idle about 3k+ RPM at full choke. 
The fact that it's dropping and eventually dies may indicate that the fuel lines are not routed correctly and it is, in fact, running out of fuel.

Hooligan

Quote from: FJ_Hooligan on June 15, 2013, 07:25:45 PM
Idle should not drop on full choke.  In fact, it should idle about 3k+ RPM at full choke. 
The fact that it's dropping and eventually dies may indicate that the fuel lines are not routed correctly and it is, in fact, running out of fuel.

Hooligan

Or the idle circuit is plugged with crud...  When were the carbs last cleaned?  I'm not following all of your posts so if this has already been done, (and unless it was not done well enough), then ignore this input.

Dan