Runaway Idle

Ok so I have a 1983 Kawasaki KZ750 LTD H4 with a Wiseco big bore kit and pod filters on it, I rebuilt the entire engine, used the Dynojet stage 3 jet kit with 136 main jets, set the timing and got it idling very rough. but it could maintain idle and ride, but would have hang throttle, it would rev to 3k and then come down VERY slowly. so I figured there was an issue with timing. I pulled the top end apart and realized when tightening down the cam caps and timing chain tensioner that it advanced my timing by about 10 degrees. So I corrected it and reassembled, now that it is back together I have an issue with runaway idle, I start the bike and it wants to spike to over 3k. I checked for vacuum leaks with ether, and made sure my throttle cable was adjusted properly and not hung up on anything and made sure my bench sync on the carbs was set correctly. Given it has a big bore kit do I need to advance or retard the timing? Also I am setting timing base on my FSM on the T1 mark for TDC but see conflicting answers on forums saying to Set timing based on F1 mark. Some clarification would be great. 

Added note when it was running before and even now with the runaway idle my vacuum sync gauges are pinging in the "late valve timing or leak at intake manifold" zone of the gauge. Again I checked for leaks and even replaced all my intake boots. If anybody has any idea I would be very grateful I have been running in circles with this thing. 

EDIT: I included two photos of the static timing I set. And I made sure that the IN mark lands between the 45th and 46th pin as per the FSM.   

Check again for intake leaks. To find one, you'll need to waste a lot of spray. Constant directed blast at suspected leak locations while the bike is idling.

The only thing I don't understand is I had runaway idle prior to rebuilding the engine and carbs. Once rebuilt and I set the bench syn on the carbs as per the FSM with the second upper vacuum hole half way exposed it did idle, but my timing chain tensioner was not holding proper tension and the RPM would hang. Once I corrected the timing it now wont Idle at all below 3k+ it makes it hard to find a leak when a cold motor on fresh bearings spikes to over 3k on start and wants to keep climbing. Is there a way I can presoak the area or force a RPM limit another way so It gives me time to hunt for the leak?

Please post an image that shows us the condition of the spark plugs.

Example:


122.5 and 127.5 Main Jets currently meter the fuel to my modified 84 ZN1100 engine, and I may try running a size leaner.
 

Here you are good sir, all new plugs at time of rebuild they have probably 2 operating hours on them.

Others may disagree, but to me your plugs appear a little rich...

Also to me spark plug 3 looks wet... Are you getting strong spark? 

As noting this symptom happened previous to anything done. I know you bought the aftermarket kit with other jet sizes but what they supply as a stage 3 might be a bit much for other parameters your 750 doesn't have. Just because you bored it a little, vacuum dynamics won't be that much more then a stock engine. You didn't mention any other head work or change of cams? Intake restriction or pods generally affect lower running pilot, 4-1 exhaust mains. Because 1983 was a sorta transitionary era, using different brands of carbs. Do You have the Keihin CV34 or Mikuni BS34's?          

While gross looking, just grabbed them from a bin. These are BOTH the KZ750 brands/types used, Mikuni to the left in all photos. Mikuni is much easier to work on and a simpler design then the Keihin that started using 2 main jets in 1981. Once you establish your poison we can proceed further. I have a sneaking suspicion while you surely addressed the jets you might of overlooked the air correction jets or perhaps something you weren't familiar with.