There is at least another character who will get the Izuku treatment. For the rest I'm not too sure. In terms of what I use it's fairly simple. Koikatsu for animating, Aseprite for spritework, Rpgmaker for the game itself and that's about all you need.
Yeah it's Koikatsu (sunshine in my case but it doesn't matter) thought it's heavily modded for the added functionnality in the studio. The steam version should work fine but you'd still need Better Repack and other mods
Next to the merchant house there's some rock you can break. Also interacting with the shack in the forest again can start chapter 3 if not already done.
Depends on how old they are. If they are from before Chapter 2 Part 3, then yeah you'll get an error when trying to play after having transfered them. Otherwise just move the global file aswell and make sure you move them to the right location and you should not have any problems.