I can't speak to all the categories you've listed but from my experience:
1. Windows: depends on the energy efficiency and features. I've replaced all 20+ windows on my property mid tier windows (nothing fancy but also not cheap like builder's grade) for $14k. All of the casings were replaced and new sills were installed where the old ones had rotted. I had this done by a large retailer that specializes in window manufacturing and installation, which is what I recommend since they can supply and install the windows with less overhead compared to a GC.
2. HVAC: Not sure what you mean by "repaired". I would recommend having coils cleaned, refrigerant charged to spec, proper safeties installed (and working) such as high pressure switches and float switch. Have your condensate drain line cleared as well. Replace all fan and compressor capacitors up front. Essentially perform regular preventative maintenance. In terms of duct cleaning, it depends on what type of ducts are installed- flexible or rigid. Flexible ducts are harder to clean and cheap enough to supply and install that it would be better to replace dirty runs entirely. Overall, I would say your HVAC costs will cost between $800 - $1500 conditional on if nothing major is wrong with the pre-installed system and most is just PM work. That is what I would charge as a HVAC contractor.
3. Flooring: I had LVP installed for roughly $4.50/sqft including quarter rounds installed and painted. Going over tile will be cheaper, just make sure there aren't any level issues which will require tile removal and flattening your surface.
4. Kitchen: Best to go to a wholesale kitchen supplier for prices in this market. They can give you a better price with your exact layout and and cabinet/counter choices. With all the renovations going on, I suspect prices have gone up since I had my kitchen replaced in early 2020. My kitchen looks similar to yours and I had shaker cabinets and quartz counter top installed for about $5k. An SS appliance suite (fridge, microwave, dishwasher, oven), will probably run you $3k, depends on if you can find good deals and/or discounts in your area.
4. Bathroom remodel: Probably going to be atleast 4k since you are replacing the vanity and all tiles. Glazing might be a cheaper option if you want to cheap the tiles.
5. Fixtures/Switches: I replaced all the switches, door handles, hinges, light fixtures for about $600. There are online wholesalers that can give you a better price vs. big box stores.
6. Paint: I've gotten paint quotes from one of my 1,600 sq ft apts for $2000 but it has tall ceilings. Best to call around.
Overall, I would say the easiest and cheapest way to approach this rehab is to have a window supplier do the windows, a kitchen wholesaler to do the kitchen, a flooring guy to do flooring and a GC to do everything else.
