Lot's of things to consider when downgrading a cage.

When you cut the forward bars out (no bars are allowed to pass through the firewall-attached or not ), make sure that the remaining pads are legal for IT (assuming they're going to the strut towers).

I don't see a problem leaving some "stumps" You may end up doing more harm than good in attempting to cut them completely off. Same goes with removing the doorbars unless you're going to the same spot. Remember, the steel has already been welded to once in those areas. Gusset the crap out of the new bars.