I will do my best to try and remember how Mission Computer does things. I work mostly with EVNEW, since my laptop is a PC, and I have a Mac at home, where I pretty much spend little to no time these days. For each ship, you need a few resources that are all pretty dependent on each other.
1. Ship resource. This provides all the stats for the ship. It's been a bit since I've fired up Mission Computer, but I do believe it should tell you what the associated resource numbers are for shipyard desc and pict resources, escort desc resource (if you allow the ship to be used as an escort,) targeting pict resource, and most importantly: the associated shan resource. The shan resource is what relies on the rle resource, which I will cover later.
2. Desc resources. These provide the descriptive text for your ship. Now, for a ship that won't be purchasable in-game, you can put whatever in the resource. It just has to exist. This is the text that will show up that tells you about the ship in the shipyard. If you want to have a large, pretty shipyard picture that comes up when you get the ship information dialogue box, I believe you attach that to the shipyard desc resource, but my memory on that is a little hazy.
The two desc resources that you need to have are the shipyard desc and the escort desc. Mission Computer should tell you what resource ID numbers are assigned to these. In fact, I think it also allows you to create them from the actual ship resource editor, but again, it's been some time since I've fired up MC.
3. Pict resources. These are simple pictures. They do not have to be in the Macintosh PICT format, I think. Typically, when I am importing images into EVNEW, I use .png files. I believe MC is okay with handling those as well. There are two pict resources that each ship must have, and an optional third.
The first is the shipyard pict. This is the square image that pops up in the shipyard. These are typically in Nova 200x200 pixels. These typically consist of a nice render of the ship in question placed on some sort of colored government-identifying backdrop. I'd imagine for the Borg, you'd probably want a nice green, and possibly some of the cool Borg spidery alphanumerics.
The second is the target pict. This is typically in Nova 128x64, I think. These are the little images that pop up in the HUD when you target the ship in question.
4. The shan resource. This is the really critical one. It tells the engine how the ship will use the sprites, where to fire weapons from, almost everything graphical about the ship in question is controlled from here. MC will tell you which associated shan resource ID is related to the ship ID. The shan resource will ask for a number of things, but the big one you want right now is called the "base sprites." This is just the sprite sheet for your cube, which you've encoded as an rle resource.
The shan resource will need to know how big each sprite is, and in what kind of a grid it has been laid out. It will need to know how many frames the sprite has. This is typically 36, but it's just important that the number of frames you created for the ship matches this number. If you got fancier with the cube, you could set it to have engine glows and running lights, but you certainly don't have to have them, nor at this point do you probably want to tackle that just yet.
5. Rle resource. You only really need to create an rleD resource these days. The rle8 is a holdover from 8 bit monitor screens, which are pretty much gone these days. This is the actual sprite image sheet. It's not important that each sprite is a square, where the x/y pixels are the same, but it is important that every single frame is the same size. You also need to create a mask resource as well. I believe an rleD resource can actually store both the image and mask resource. EVNEW does it this way. I am not sure if MC does as well off the top of my head.
To create a mask resource, you will need to select everything that is black in Photoshop or some other image manipulation program with what is typically the "magic wand" tool. Set your tolerances so that you select everything that is black, but don't get any of the actual sprite. This might be difficult with the Borg cubes. Cut this black out and paste it as a new image. You should get white holes where the ships used to be, and a big black cookie-cutter looking thing around it. Flatten the color depth to one-bit, or pure black and white.
You can create a second rleD resource for the mask, or as I said, I believe an rleD can store both the image and its mask.
Once you've gotten all of these resources together and put them in concert with the correct associated ID numbers, you should hopefully stop getting those error messages. I wouldn't advise uploading incomplete plugs to the add-ons directory, as the moderators don't particularly care for that. There are various services that will do basic file hosting for you. I believe Dropbox is a good one, but since it's blocked here at work, I can't provide a solid link for you.
Once we get the ship working in-game, we can start adding in ways to make the ship appear as an AI controlled ship or fleet of ships, and add in weapons/outfits. Much fun.