Consistency is best, but there can be a certain consistency in non-uniformity. Are the stained windows within one room? Are the french doors? One option that you have that also has historical antecedents is a stained door with white trim, windows/ trim, and baseboards, and you could do this throughout the house for a certain amount of consistency. If the windows with the stained trim are all in one room, perhaps that entire room could have stained woodwork. Note that doing stain grade doors throughout the entire house can get relatively pricey. The key is to have a rather consistent plan or hierarchy and following it.

As another option, repurpose the opening for an additional function This wine rack hides access to an exhaust fan - if necessary after removing the tiles, two screws retain the box Or, let the trim become framing for art - a poster can be wallpapered onto the door

Re "My focus would be making it homey vs trying to achieve a historic general store feel." I dont think the 2 are mutually exclusive. Is there any commercial aspect to this OP? If not, no you certainly dont want people thinking its really a business or walking up on your porch trying to get in, but on the other hand it does have a history that should be embraced and not be overlooked - the long time locals certainly wont! So yeah I do think navy, dark grays, all the contemporary "mud" colors--- are much too somber for this building. Does not fit either its history OR its architecture. Those same colors might look great on a big, stately Victorian former boarding house, funeral home or some such - but not your more rustic 1920's facade. Have you connected with local historical society people? No of course pleasing them is not your intention - it's just they might have some thoughts/ideas on it that you havent considered.

Not sure what you mean by removing built insYou do realize if you remove anything sitting on the floor you will need to repalce the floor since the chances of finding the matching flooring you have will be impossible . I think leave the FP for now and work on the other issues you ar edealing with . The FP can be painted or not down the road.Is the furniture you show yours? If so IMO it will not suit a painted FP.