There's also a workaround you can do in hex, but keep in mind it'll probably destroy the difficulty curve somewhat. (especially if you abuse "shard shifting", which I would very much avoid doing if I were you) If you feel like Purple and UnNamed might be too difficult, it's worth a shot.
Once you have a suitable hex editor, open the hack up in a hex editor and go to 0xCE91A in the hex editor, and change the next four bytes to "00 00 14 E0". This should fix level evolutions, but it dosen't fix the stone problem.
To fix the shard evolutions, go to 0x126C4D and change the D9 to an E0. That should allow puppets to evolve into the shard forms without the use of the national dex.