So how do I multi map/equip?

How do I bind multiple attacks on a single button?
And/or how do I equip multiple copies of the same weapon/passive/whatever?

Also:
How do I repulse/destroy mines since they are projectile immune?

Suggestion:
A search box for the shop.

Currently the game does not support binding multiple abilities to a single button. There are several third party programs that allow for this functionality if it is desired. This is a feature that is fairly high on the priority list.

AutoHotKey is a popular one, though I haven't used it myself.
http://www.autohotkey.com/

You can't equip multiples of any piece of equipment unless it is marked as a "component". Components are things like Thrust Modules, Shield Regen/Max Modules etc. Allowing for several instances of certain abilities to be active on a single ship would break the game.

Mines are treated like any other projectile in the game. There are several abilities that can block/destroy/move projectiles in the game.

Certain projectiles are immovable (i.e. energy projectiles like photocasters), so you won't be able to repulse/snare them.
Certain projectiles are indestructible (i.e. dark matter orb), so you won't be able to destroy them.

I will deploy AHK. I use it daily for other tasks, mostly on the fly spell checking across all inputs (I don't think I've hit shift when typing "I" in 5 years lol.)

Might I strongly suggest you start parring down all these part restrictions and caveats? :(It really guts the customization in my opinion.

I mean seriously, for the placement of any part in any slot, how many caveats are in play total?

Cost, research, class, type, component status, unique status, etc. Edit: perhaps you could link the shop and research goals to the empty slot at any given time? Like a database query: Based on current options, what parts in the game could fit here (Hover mouse or maybe a corner icon?) that I haven't bought or researched yet.

Unique and component need to be merged. If you only want one of x per ship, fine, make it unique. But really as it stands I'm not allowed to make anything approaching even contemporary naval vessels, let alone deep future space craft.

The decision to focus on uniform armament type was a critical point in the development of naval warfare. In fact that's the exact reason why you know the word "Dreadnought."

http://en.wikipedia.org/wiki/HMS_Dreadnought_%281906%29#Development_of_the_Dreadnought

Basically as a rule of thumb, I as a player should be able to build a space ship equivalent of any deployed naval vessel in history.

Submarines for example, stealth strategic missile boats. Or aircraft carriers, slow moving drone ships with anti-missile/mine point defense and phalanx guns but unimaginable cost.

And it's also worth pointing out that anything you do to implement a realistic aspect of space combat is likely to be unique and therefor innovative.

http://gizmodo.com/5426453/the-physics-of-space-battles

http://science.slashdot.org/story/12/02/20/2024245/ask-slashdot-what-would-real-space-combat-look-like

If balance is an issue then make a different suite of ships and options available for single player. (Like how MTG does type 1 and type 2 and extended.)

I want variation carried to the eve online degree and further

You let people CREATE and they will eat that shit up. Citation needed? Minecraft, Gary's Mod.

I like the idea about linking unavailable parts into the actual customization screen. I could add them to the bottom of the Equippable Items list for the node while you are equipping it. They would be grayed out, and if you click them you would get a pop up with the equipment info and an option to purchase. What do you think?

That would be outstanding. Profoundly helpful.