The entire evolution problem is because hemo forgot to hex edit something out of regular FR/LG...
namely, that evolutions into post-national dex pokemon are blocked until you get said national dex. in normal FR/LG, this only affects two pokemon (golbat and chansey), but in touhoumon 1.8, every shard evolution bar one (attack keine) is post-national dex.
yeah.... why hemo didn't edit that out is a mystery.
I know there's some hex to change this, but I forget what exactly it is... (and changing it without changing the shard locations leads to silly things like having attack sanae before the second/third rival fight)
*edit* nevermind! found the hex codes!
if you want to fix regular evolutions, go to 0CE91A and change the four bytes to 00 00 14 E0. (this only is needed for the PC98 puppets, if you encounter any)
if you want to fix the stone evolutions, go to 126C4D and change the D9 to an E0. That should fix the problems you are having, but keep in mind that a lot of the shard forms completely destroy the maingame.