RE: General port timing guidelines?
If you visualize the piston area from the top of the upper ring land to the top edge of the piston itself, I remove half of that. That leaves enough material to support the ring land. I have done this on numerous engines without problems. Chamfer your cut of the piston top, with two things in mind. 1. Good flow out of the port. And 2. Take only as much as absolutely necessary because this lowers the compression ratio.
I don't know why some engines don't completely uncover the exhaust port as in your case, but modifying the piston to allow the port to open fully will definitely gain some power. On one engine that I did this to, it gained 800 rpms!
As a side note, checking to see that the exhaust port is opening fully is the first thing one should do when leaving out the base gasket and/or machining the bottom of the cylinder to increase the compression ratio.
AV8TOR