With Homestuck shirts, I've done iron on transfers, which look good, but peel up on the sides after a few washes. Also you don't wanna' put it on a shirt with any kind of stretch. I ruined my Rose shirt that way. 3:
I usually just prefer to use fabric paint and a cardstock stencil I made. If you're doing regular fem John, then that might be a bit difficult depending on your art skills. If you're doing femtier, then it'd be easier.
For makeup, depends on your headcanon, but I think keep it natural so it looks like you're not wearing any. Obviously, wear some, but keep it natural. I don't think girly John would bother much with that.