I recently did a 203K rehab in Chicago on our first house hack (a 3 unit). I'm not an expert in the field, but my perspective could help. Are you house hacking this property or using it purely for investment?
1) @Jonathan Klemm can give you solid info on this.
2) AC is practically a necessity to get top rents nowadays- especially if you plan to MTR or STR in this building. If you are already doing ductwork and soffiting for heating, the cost of adding in AC is worth it. I think the demand for AC will go up as the years continue, so doing the work up front will make your units more attractive for years to come.
3) We kept water heaters in each unit, but made a utility closet to get them out of the kitchen. I've heard tankless water heaters are an option that works well, but I have not experience with it personally. Relocating to the basement would be a great option if you need the space to make a better floor plan in the units. If not, utility closet might be a cheaper and less labor intensive project.
5) Will getting rid of the chimney help in a major way (space, etc.)? If you get high efficiency furnaces (and therefore don't need to vent through a chimney), you can just close off the chimney and have less cost to demo it.
6) In unit washer and dryer are becoming a must for for MTR and STR. If you plan on making a unit STR, then you could do one unit with washer/dryer and the other two units could have a common space for laundry. I use a combo washer/dryer unit that is electric and requires no venting (everything is condensed to water and drained out through regular plumbing). The only issue with the single units doing both jobs is that they spin very fast and cause a lot of vibration if the floor is not sturdy.
8) A duplex up 3/2 or 4/2 could be really nice for LTR, MTR, or STR. If the bedroom sizes come out too small, then I think it is better to keep it 1 bed/1bath in the attic. I think its better to have spacious rooms since renters will pay higher prices for a solid sized bedroom as opposed to two small bedrooms.
Congrats on an amazing property! Do you already have plans and permits, or are you in the start of that process?