I would leave the transfer ports alone, except for raising them to get whatever timing number you are after. And even at that keep the original angle in place.

To the best of my knowledge, yes, there are 3 transfer port designs and you have the newest. I have a Homey 30cc that I hopped up, and it turns an APC 16 x 8 prop at 9400 rpms. Not bad, and it has the oldest transfer ports. I bought a couple of cylinders with the larger, second design transfer ports, but still haven't gotten around to trying them.

If you end up making your carb adaptor opening so large it breaks into or gets too close to the pulse hole, you can close that hole with epoxy and run a pulse line from the block to the carb itself.

Have fun,
AV8TOR