Epic Ships
Let me start by saying that I enjoy using your squad builder.
I have noticed that epic ships with multiple ship cards do not function well within your squad builder. One issue is that each card gets a modification option even though only one is allowed for the epic ship. Secondly, Ordinance Tubes bonus does not translate to both halves when selected for one side . This means that a player can not option in a missile or torpedo to one half of the ship. I understand that these are due to coding restriction. Have you considered that since the two cards for an epic ship can not be taken separately that for the purpose of your squad builder they should be treated as a singular card? By doing this you resolve both listed issues since all upgrade options will list at once and be nested together.
Huge ships with two halves can't be treated as a single card, since you have to track which upgrade cards belong on which half of the ship (which is important for dealing suffering critical effects, and discarding upgrades when halves become crippled).
I have been thinking about how to associate ship halves together, and it keeps being more difficult each time I look at it. I'll keep thinking about it, though, as I do want to solve this problem.
Is this issue still being developed on? This squad builder is my favorite by far but this issue keeps me from using it for Epic list building.
I have not really looked into this. I keep hoping for an Epic FAQ update from FFG to clarify some of the modification weirdness and help with nailing down rulings, but also the code is really not amenable to supporting weird stuff like Ordnance Tubes. So I don't think support for this will be forthcoming any time soon.
If I do a rewrite of the builder engine I will keep this in mind.