God, the original prt.Mimi sucks ass.
No matter what you do, you're going to get some misaligned textures, in fact even the original Cave Story had some; I guess Pixel just didn't care. Also, the tile set itself looks bad, overall.
He definitely learnt from his mistakes, though, since prt.Cent and prt.Jail are so, so much better.
please keep in mind that even though its cool you're making a cs mod, we dont owe you anything. a lot of us forum folk would love to see a mod from you, but you need to be the one to take lead and generally avoid asking people for help with big things like TSC and core ideas. thanks