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Well guys I finally got it started (after the usual mucking around) This is a cold start on full choke, the timing was roughly set statically so still need to sort that out.
I was very relieved when it fired up straight away - the first start is always the scariest moment !
(651) 1973 Kawasaki Z1 900 - first start up after rebuild - YouTube

Well that was easy!!!

The one step in a project that you hope is anticlimactic!  Well done.

Better than sex (At my age  )

Well there has been a couple of hurdles as I attempt to get the ignition timing worked out.
Firstly I found some oil leaking into the ignition housing, Immediately I think the seal must be leaking.  No, its not that, I had actually forgotten to put the seal on 
ok, seal on, start her up - the idle is at the F mark after some adjusting of the plate (and no more oil leaking)
Rev it past 2500 and the strobe light is shining on something, but no mark that I can see.
So I read some of the installation instructions and remember that the Z1 has a 5 - 40 degree advance unit and the later bikes have a 20 - 40 degree advance unit.  The Dyna S elecronic igniton requires the later unit. 
I dug around in the ignition box of bits and found a later advance unit;  Its got a bit of corrosion on it, but you can see the difference. 
 

On your Z1 advancer....is there no mark under the pawl?  My manual says it should be 5 deg up to 1500 rpm and 40 deg above 3000 rpm.

I had this same issue running a Dyna S ignition I just swapped in a later advance, but you could contact Dynatec and get the rotor for the early advancer.

Dyna-S Electronic Ignition DS2-1 - Kawasaki Z1 KZ900 KZ1000...
If you have a 73 Z1 or an early 74 Z1A, we may need to supply a different crank rotor. Up through engine number Z1F-32817 kawasaki installed a 5/40 degree mechanical advancer (normal fire mark is 5 degrees then advancing to 40 degrees). If you have one of these on your engine, please enter a note in the special instructions to replace the standard rotor (3 rotor) in the Dyna-S with one special for these early bikes (3A rotor).)
As many advancers have been swapped from bike to bike, please check before ordering.

wrote:

On your Z1 advancer....is there no mark under the pawl?  My manual says it should be 5 deg up to 1500 rpm and 40 deg above 3000 rpm.

There is no full advance mark on this advancer.
If the timing light has idle on the F mark then it *should be* 40 degrees after 2500 rpm I'm guessing. 

wrote:

I had this same issue running a Dyna S ignition I just swapped in a later advance, but you could contact Dynatec and get the rotor for the early advancer.

Dyna-S Electronic Ignition DS2-1 - Kawasaki Z1 KZ900 KZ1000...
If you have a 73 Z1 or an early 74 Z1A, we may need to supply a different crank rotor. Up through engine number Z1F-32817 kawasaki installed a 5/40 degree mechanical advancer (normal fire mark is 5 degrees then advancing to 40 degrees). If you have one of these on your engine, please enter a note in the special instructions to replace the standard rotor (3 rotor) in the Dyna-S with one special for these early bikes (3A rotor).)
As many advancers have been swapped from bike to bike, please check before ordering.

 

I have an early and later advancer units in my box of ignition stuff - these parts were taken off about 20 years ago and put in the box.
I have a funny feeling that if I have a later advancer unit in that box, then that was most likely what I was using with this Dyna S ignition.
I have no idea if the rotor is the #3 or #3a - cant see any markings on it.
I will just swap the units over as I have now cleaned up the later 20/40 degree unit and see what happens - thanks for the info Moose.

ok, I have swapped the later 20/40 advancer unit in.
fired it up, I had to wind the idle screw back because it idles much better now.  Once it had some heat and was off the choke I got the timing gun on got it fixed on F at idle and full advance mark at 3000 rpm - no worries.
Engine is idling nicely between 1200 - 1300 which isnt bad considering it has 430 lift cams and 38mm carbs on it !

After some fiddling I have backed the timing off 2 degrees to 18 - 38.  Tuning advice on APE site suggests no more than 38 degrees for a modified KZ engine.

I have tried to upload a video of the bike going down the road but it wont accept mp4

 

I have been slowly going through the laundry list on the whiteboard fixing all those stupid little things that crop up when you actually try and ride the bike.  
Put some air filters on instead of the velocity stacks so I can keep shit out of the carbs and intaks.
 
The fuel tap had a slight weeping to it when in the on position - put a new O ring kit in and it seems good now.
 
Did a bunch of other things as well, only 1 thing left and that is a helicoil required in a 6mm head thread.

the $50k sale of the Z1 at Mecum's auction on the weekend would certainly lift the spirits of any 72/73 owner.
(started a thread on that in Other bike discussion)