If this is a conversation versus a monologue, what I’d do is record both sides in the same room or within earshot of the two speakers, so they can hear each other and judge their delivery timing. If the replacement lips person can keep their head still, it is a huge help. Some type of strap or neckbrace or padding to keep the head immobile will be helpful for this.
I did this gig once with analog tape and a simple Grass switcher and I put my replacement mouth person on the carpeted floor, on their back, with carpeted apple boxes kind of wedging his head so it would stay still. Set a soft edged oval wipe around the lips and done.
The rest after that is cake in plain old FCP. Just put that guy on another layer, mask him off with a matte generator or wipe, and keyframe the positon, rotation, and scaling to taste. You wouldn’t necessarily need AfterEffects for this at all, on the primitive Conan O’Brien-type level.
If the head (and thus the mouth) won’t stay still, then the motion tracking and matching abilities of AfterEffects or Apple Motion become needed.
Something you haven’t yet considered maybe: teeth versus no teeth, and how much interior mouth you want to show. You can look up the old Synchro-vox technique used for Clutch Cargo and Space Angel, basically, that was using special colored lipstick and chromakeying the lips over still animation cels in realtime. The teeth generally didn’t show. The actors listened to pre-recorded tracks and lipsynched to them to get the mouth shapes done.
For a more realistic look, you’ll show more interior mouth. A well-known example for this would be the opening title sequence of singing lips from The Rocky Horror Picture Show…
(By RKOoooooo...) But I digress…
…That look in “Rocky” can be a little too real and detailed, and depends on geat dental work and etc. to look good in closeup. In a medium to wide shot, maybe not as big a problem.
Just pointing out that your look has a lot of variables to consider, and that will drive your choice of techniques used…