Think you will be pleasantly surprised with the direction you are headed ..
Just consider trying to get a better squish band machined in that cylinder, which unfortunately drops the cylinder even more exercising your die grinding skills even more yet. I haven't come up with a solution to the floor of the exhaust port being low even before trimming the cylinder base though. Maybe some "new" folks with different idea's can do better. You know the definition of insanity is....Just as a thought, the old "Madsen" approach to gaining x-sectional area on the transfer might work too....they decked the cylinders as most do to be able to first get a nice squish band and compression, then machined "ramps" or wide grooves into the top of the piston so the transfer timing or blow down was more reasonable & more cross section open when the piston was at BDC. Many of the "hot rodder" type deck the cylinders here in this paradigm and since the lower edge of the transfer is now that much further below the top of the piston at BDC, creating a "square" edge & resultant turbulence effectively shrinking the cross sectional area ....most go and raise the top edge of the transfer to regain that area...with crazy small blow down numbers which is a bit counter intuitive if you come from other two stroke worlds, its just the x-sectional area gain over comes the issues with timing. Theirs was a compromise to that problem.