How to HVAC service 3 floors without ducts in roof

First, realize that with a single zone system and multiple floors, it's difficult to get the temperature correct everywhere. Also, since you mentioned this was an attic space, you're likely against the roof and getting heat from every wall plus from the computers and people in the space. In short, you're fighting a losing battle.

I've got a similar challenge, though not to your extreme, and here's what I have done. First, learn how to adjust the baffles on the ducts. In the summer, you want as much as possible going to the high floors, and the reverse in the winter. Get someone to feel the air coming out while you're pushing the baffle all the way to one side or another. For me, it made little difference until I pushed it all the way.

Next, exclude any rooms you don't need to heat/cool, e.g. a guest room or storage space in the basement. Shut the door and close the vents to reduce the effort you're putting on the HVAC.

Finally, I swapped out my return grille with models that accept a filter (they are hinged and open after releasing two small clips). These return grilles are special orders from the big box stores, but they carry them. I still leave a thin blue "rock catcher" filter directly on my HVAC blower itself. And I put a filter in every return except the upstairs in the summer and downstairs in the winter. The idea being to suck out as much air as possible from location that needs it.

This means that switching between heat and cool is a process, flipping the baffles and swapping in and out filters. But a little effort is better than a lot of sweating.

One last suggestion, since it sounds like you're running a small server farm in your attic. Either move that down to the basement, or consider replacing the window unit with a ductless mini-split system. You get to see out the window, and these systems have configurable thermostats.

I would guess that modifying the duct work in a 1920s masonry construction home will be prohibitively destructive and involving removing or damaging irreplaceable trim that contributes to the building's character.

Mini split heat pumps:

An alternative, which will not be inexpensive but may be significantly less destructive, would be investigating installing a multi head mini split ac unit with one head in each bedroom. Such a unit costs perhaps $2500 to $5000 for the unit, installation extra and depends on the difficulty of install. If you live in a heating climate, especially one with cheap electricity in the winter or might install solar and have sunny winters, you should likely invest in the heat pump versions. Models are available that operate down to -13 F now (Mitsubishi M-Series) in single head. Supposedly multi-heads that operate that low are coming out this spring.

Advs:

Individual temperature control for each bedroom - Really high efficiency available for both heating and cooling - Avoid destruction of interior trim

Disads: - Potentially a lot of $$$ - Still a newer technology in the US (used all over Europe and Japan). If you plan to sell soon, recovering your investment at resale could be a challenge - Some people hate the look.

Other than minisplits:

Air leakage:

I'd suggest you have a blower door test performed. All the insulation in the world doesn't matter if you are changing over the air in the house too quickly. If you didn't air seal the attic before filling it with cellulose, you could have this problem. An infrared gun on a cold night can help show these leaks too. Insulation installers will say things like seals in air but cellulose, fiberglass insulation, and mineral wool insulation are actually very air permeable. If you find that is the problem, you could move insulation out of the way in the attic to use canned foam (get a commercial gun, much nicer job to do than with home depot cans). If you can't move the insulation, you could install a vapor permeable sheet membrane like Tyvek or a smart vapor retarder like IntelloPlus on top of the insulation to block air movement. Do not use a vapor impermeable barrier like black plastic or visqueen (clear plastic); you could trap moisture and cause a mold problem. Attic access hatches are also causes of large volume air leaks. There are special hatch covers you can buy or build to address this problem.

Duct work in unconditioned space:

Do you have any ducts in unconditioned (uninsulated) space like an open crawl space or an unconditioned attic? If so, you could be losing huge amounts of heat to the crawl space or attic. If your ducts are older, they likely aren't air tight either. You could use specialized foil tape or duct mastic to seal the joints and you could insulate this duct work, though it won't be fun work. If your ducts are really leaky, you could get big gains in system performance from this work.

Humidity control:

Have you measured your humidity when your system is running? If your humidity is high in the winter or summer, you will feel colder or hotter. Your humidity could be high in the house for many reasons (improper shower venting) but dirt crawl spaces are a big source in the summer (not in the winter so much). Seal off the dirt crawl space to eliminate humidity, mold spores, radon, etc. from getting in the house. A radon membrane company, in areas with radon, might be a cost effective contractor to use.