Yeah, that's the approach I'm gonna take. Would go with two 'hacked' versions to accommodate for the spreading of Doc Robots over all the stages (1x8 stages instead of 2x4 stages).
In that case I'd simply start removing the midway Doc Robots in their stages in one version, and edit the regular Robot Master stages that don't have a Doc Robot variant for the other version. Then I'd need to make these four stages accessible once the Doc Robots appear, so you'd have to switch ROMs/patches when they do.
Oh, of course I could also just switch between an unchanged/changed ROM, if you're gonna do all the Doc Robot stages on the changed ROM.
Doing it with two ROMs seems unappealing to me. I'd like to know if maybe I could split up the two halves of Doc Robot stages, or even change them into final stages so I have more freedom in deciding their theming.