Yea, That doesn't look right. Are you sure that is the correct piston for the cylinder? Also, you need the chamfer the port edges before you run it. They look really sharp and can snag a ring.
Thanks for the squish guide.Most new motors have the exhaust port higher than the piston at BDC. I've seen a few motors where the transfer ports are lower than the piston. Not ideal but works fine.
Squish is normally > than 1% of the stroke length.