Progress so far...

Pilot jets MUST be PERFECT in appearance to work correctly.  Any defect in their appearance can ( and usually will) have a detrimental affect on the idle.   When re-building the carbs replace all 6.  Replacing only those that are "beggared" is not prudent.

As always:  Popping and Farting is almost always a blockage of some form in the main idle port.  Given that you've used the Cleaning Tool and the issue continues I would suspect some tiny pieces of brass from the idle-jet removal, have found their way into the system.  Most, don't truly appreciate how small a piece of foreign  material it takes, to mess things up.  No solvent will correct this but repeated cleaning with solvent and compressed-air should deal with anything stuck in the galleries.  This is why the tool was designed to flush Backwards to the flow and out through the large openings (when the jets are removed).  Under no circumstances should compressed-air ( or fluids) be applied in the operational direction of flow.  Doing so can ( and usually does) jamb crap into the idle and transition ports.  If this crap happens to be tiny shards of brass from butchered jets, they can be difficult to remove.  The instructions for the tool recommend that the cleaning fluid be caught in a (clean) tray so any flushed-out debris can be examined; giving you some insight as to what was causing performance issues.
Slow to return to idle can be due to the Sync.-adjuster screws be turned in too far; causing binding on the linkage ball-joints. 

Nice workotherwise - Bike looks great  !
  

Thanks Scotch! Ok I'll have another go at those idle ports then. I guess I should have replaced the last 2 pilot jets.   That'll teach me to cheap it...
. I'll have a look at the linkage ball joints too while it's all off. The slow return to idle only seems to happen when I turn up the idle speed screw.  Is it because the idle speed screw is so far in I'm possibly beyond the idle circuit slightly ?

I couldn't always catch the cleaning fluid very well. Not knowing these carbs very well I tended to spray myself with it half the time.

I'll hopefully get the carbs off again today...I'll keep you posted... Thanks again!

 

Ok so I spent the whole day cleaning the carbs, I had good solid streams of carb cleaner flowing though the idle and transition ports. I just mounted them back on the bike for a test ride which was short lived. It's now running like crap.   . It wasn't firing on cylinders 5 and 6. So not sure what I did wrong with that carb. Strangely I spent more time cleaning that one that the other 2. 

Not sure what I can do other than wash and repeat?

I've been setting the idle mixture screws as per the manual 1 and 3/4 turns out, is this correct?

Most, if not all owners have learned that the Manual is wrong with this point.  It's generally accepted that 3 - 3.5 turns out, is the starting point for pilot screws.  From there you can fine-tune with a "Gunsons Color Tune", by the spark-plug color and/or by "ear". 

I guess I'm living proof that it wasn't all owners, though if I am the last one to find out the manual was wrong, maybe it is "all" now. Luckily I did some browsing over this site and found the 3 to 3.5 turns out just before refitting the carbs... I only cleaned carb 3 this time, I made sure there was fluid squirting from every orifice....of the carb.

I gave the  (nearly new) plugs a good clean in case they had fouled up as they do get a little sooty. That was a lie.... they get very sooty!.
Anyway. Still wasn't running on 5 and 6. popping and farting as well. I'm starting to think it may not be the carbs after all. I tried to run the bike a little longer to see if I could get it to run... and as it heated up it started running on all 6, though number 6 was the coolest for sure. I took it out for a run to see if couldn't rev it in to submission. Strangely it did start running quite well at times and even started to idle...almost.

Happier I put it away for the night thinking maybe it's fixed !?..... But...no. I tested it again today. Still intermittently cuts in and out of running on 4 to 6 cylinders. Riding back through town, I was getting some strange looks as it popped and banged quite loudly sometimes.

First ride of the season tomorrow. So dissapointed the big Z didn't make it.

Not sure which direction to go in now. The coils are fairly new, the HT leads new as well, the stator is newish also. Regulator rectifier is old and probably the original. I'm stumped as electrics are just Chinese to me.