Sorry about the silence for the past while, I was stuck trying to think of a better layout that isn't confusing (thinking that mounts and types are one list). But now I think I've found a solution (partly inspired by MoO 3's ship design)
Since you can only select one type and one mount, but as many modifiers as you want, I'm going to change the type/mount selection from a list to a drop-down. The selection window will be split vertically. On top left (under the type buttons and equipment name) will be the two drop downs (type and mount). Under that will be a list of modifiers.
On right will be the information for the selected equipment, listed vertically, and on bottom right will be the confirm/cancel buttons.
I think this approach will reduce the visual clutter (three lists makes for a lot of clutter), and reduce confusion.
I also started fleshing out the design screen, I hope to have both equipment selection and design screen done tonight! The next thing on agenda will be the star system/planet data files that I mentioned earlier.
Speaking of which, I realized another thing, what if you want a blue star to have up to 5 planets, while yellow have up to 10? That can't be done due to how the galaxy setup is done. So I will remove both black hole slider and min/max planets UI, and put those into the star system/planet data files.
I also plan on adding race's home system setup where you can specify what type of planet your race starts on, as well as if it follow the star system's random generation, or a pre-set system that you specified. An example would be Human, and their system would have 9 planets (including pluto), with the third world being the homeworld. So that will give the modders ability to specify starting systems in a more fine detail.
I plan on using that system for special systems, like the "Beyaan" system, that allows me to specify unique systems for lore purposes.