1. I don't think that you can do this normally with JCS. You might be able to get the same effect if you used a combination of zapS' new tools: J2L Tool, J2T Rearranger.
When you use the j2t rearranger, it will give you a file that can be used with the j2l tool to swap out certain tiles for other tiles. I haven't gotten around to trying it myself, so I can't give you much more help than that, but I think it could do what you want.

2. I'm afraid the number of layers is currently limited by JJ2 itself. It's pretty much impossible at the moment to add more.

3. Jazz 1 keeps all the sprites in a different way than JJ2. Instead of a single sprite archive like JJ2, the level files contain whatever sprites are needed for that level. I think J1E will let you view/edit them, but I'm not sure if it has an export function like JazzSD