Bike will not run smooth on idle.

[FJ_Hooligan]

The fuel pickup for the choke circuit is on the side of the float bowl near the bottom.  It is metered by a tiny orifice which is easily clogged up.

You will need to pull the float bowls and clean this obstruction.  You will see a hole on the side of the float bowl near the bottom.  This is connected to a tube cast into the side of the bowl.  Inside of that hole is the orifice.  It is clogged.  Also check the #3 and 4 bowls.

You failed to mention that the miss was with the choke on or this would have been diagnosed immediately.  The advice you receive is only as good as the detail you give.

More detail is provided on the Description of the Mikuni BS36 carb in the Files section: http://www.fjowners.com/index.php?topic=658.0

[Cass]

Thanks for the link it is very useful.
I think I possibly had a couple of problems as previously as I stated it would only start on two cylinders with the choke out but once running and the choke was in it would continue to run on two until I opened the idle jets right out and it would then fire on the second two. Once running with the choke in it would back fire when throttling off going down a hill so obviously over fueling. Open the throttles half to full and she ran really well. I think as several have suggested there is a knack to cleaning the carbs if they have been sat as long as mine had (7 years) and I have still to learn it. Carbs are off again this weekend so my mate can Ultrasonically clean them and hopefully this will clean out all the crap that can't be seen down the little orifices.
Thanks again and I will update you once I get them back and on the bike.