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.
The air in your duct work is cold because it is running through the attic which is not heated. There will be some air flow through the ducts because they are not a "sealed container" they are designed to move the air in your home.
As for the DIY project if your covers are metal I would suggest using a magnetic tape or adhesive sheets to attach them. Or they make covers:
For the ceiling registers you will want to make sure the magnets are strong enough to hold material tightly.
Best Answer
Condensation is probably the result of uninsulated ducts running through uninsulated cavities in your home.
The solution is to find out what section of your ducts this is occurring at and either swap the ducts with insulated ones or insulate that section of your home.
I recently learned this about my home. I had uninsulated duct work in the uninsulated/not sealed crawlspace underneath my house.