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Hi i know we have been over this fault before some advise please.I finally got the Scotland bike going new valves inlet manifolds and lots of money ,cleaned carbs and you can see all transfer ports clean when you put fluid though to test them set mixture screws at 3.5 turns still have my old fault missing just off idle. Its like a coil or lead is breaking down they are new and where on the bike when i brought it no markings on them for +/- .Turned the mixture half a turn more and the fault goes away starts with choke idles smooth cold but when warms up starts idling rough and its too rich .I was reading the add on eBay for old school card rebuilds and he was saying about the choke lifters are different and if 1 is put around the wrong way it will cause the carb to be rich i have a spare set of carbs in bits and i cant by looking see any difference. when i putt the set together that are on the bike i made sure the choke lifters have free play when the choke is off . I sold the other z1300 to help pay to get this one on the road any advise would be welcome i will even send my other set overseas to get this fault fixed thank Graham.

You've done a lot of work here Graham and unfortunately this also complicates diagnosis when there's a problem. It's always easier to make a change on one thing and then check to see if the "fix" worked. Attacking many different areas at the same time can really task your ability when an issue shows up. So, lets talk one thing at a time.
New Valves- I'll assume that the seats were cut in the cylinder head and the valves shimmed to the maximum clearance. I say that since new valve jobs need to seat in and if the valve clearances are set to the tight side and not checked in the first 100 miles, they will probably be stuck slightly open. So in this case check the valve clearances to rule out any issue due to tight valves.
intake manifolds- Are they properly aligned? you can't just remove and replace the maniifolds. There is some wiggle room on the mounting screws manifold to rubber manifold boot. There is an alignment tool for installing the rubber manifolds. What to do now is to test for an intake leak. I prefer a small propane cylinder (torch size) take the nozzle off the end and put a piece of rubber hose over the end. Start the bike, get it warm, then start leak checking the intake from the bottom side up. Propane is heavier than air. You only need enough propane coming out of the end of the hose to just feel the cool effect on your cheek. An increase or decrease in idle speed tells a tale.
I don't think it's a choke issue. A failure in the choke will stall the bike for sure.
I still think it's a transition port issue. You're problem is right where the idle circuit is being taken over by the main circuit.
Although, I wouldn't rule out a bad plug or lead or coil, but if somethings off with those three items you're usually dead on that cylinder above off idle.
My money is bet on the transition ports.

Thanks KB i think your right with the carbs i have just brought a ultrasonic cleaner ill run them though that and use scotchs tool. I put a new set of valves in because the lying son of a bitch who sold me the bike had ground a inlet shim the valve and the keeper to get clearance and put it back together with silicon: : i have put a complete set of shims 2.80 and set the clearances at 7 and 9 thou so plenty of adjustment for the future.Fitted a secondhand inlet cam another radiator new hoses thermostat etc and did your zrx1200 fan conversion thanks to you and just fitted brembo calipers so i am so deep into it i have to keep going thanks Graham.

Stripped carbs on the weekend put them in my cleaner and used scotchs tool to flush them. Balanced carbs tonight and took it for a run its going the best its ever had thanks for the help KB and Scotch did a lot of reading of old threads on carb faults a great help cheers Graham