Oh yeah, forgot about the head pics. I just re-looked. I see that your piston has a positive deck height also. I'm not certain on this, but I've done a lot of reading. Most people don't like to run a positive deck height! It usually makes things screwy with the squish and the combustion chamber volume. Which I thing is exactly what you are experiencing! It's also not good to have the ports not fully open at BDC. The piston should ideally sit at the bottom edge of the ports. I'm hoping you are not running into the same problem as Josh over at Scooter Invasion. He is talking about scraping the cylinder before even installing it because the port timings are so far off they are not fixable! I think he may have a cylinder by the same manufacture as yours.
If you can take some real precise measurements, I'm sure we could get one of the guys on SI to run the numbers through the software for you. You may end up have to raise the jug up to get rid of the positive deck and allow the ports to fully open. Then either run with no head gasket and/or shave the head to bring the squish down to where it needs to be. You may also either have to run a different head or have the combustion enlarged a bit depending on how much may need to be shaved.
The measurements I think you need to run the numbers are deck height, squish, port heights from the top most edge to the top of the cylinder, port opening height (from bottom edge to top edge), and possibly head gasket thickness. Ideally, you want these measurements to the tenth of a mm.