1. Adding phases is not trivial. I think someone put out a library mod to help with that, search "phase"
2. There should be some discussion around this in the discord. There are a number of ways but the most optimal way is not quite working yet. I think the current best way is using sublevels. Rex would know more. I think there is an open source mod that adds a biomass node or something you could look at
3. Possible but not generally a good idea because other mods probably use those parts. Modify the schematics that grant the recipes for the parts