Hi,
you've done really good work. Thumbs up
I also have some Jawa bikes, Jawa is still very popular in Czech Rep. Now I'm going to build theJawa "Californian" almost from nothing
Here you can see some photos of my bikes
http://longr.rajce.idnes.cz/Jawa_50_555/
http://longr.rajce.idnes.cz/Stadion_S_11/
http://longr.rajce.idnes.cz/Jawa_350_354_kyvacka/
http://longr.rajce.idnes.cz/Jawa_500_OHC_Kyvacka/
Maybe I can give you a hint about the ignition. I was not sure from the photos, maybe you did it.
You have a two-outlet coil. Could be used for two cylinder bike. But when you're using it for one cylinder, you have to ground the second outlet. Use the high voltage wire and mount the end under some screw on the frame. If you won't do it, the coil will "die" after some time.
And my best experience with the ignition timing. I realised that the best timing of spark for classic petrol (European octane number 95) is 3,6 mm before the top position of the piston.
Good luck with continuing