What a surprise Chron, why do I always have to do the countless things you ask?
HpRunningLight07, 08 and 11 are inside the ship.: correct, and I assume they're there for a good reason. I personally checked ingame where to potentially put them, but haven't found any relevant placement. Feel free to suggest them if you wish.
HpDocklight01 and 02 should be swapped with HpRunnignLight09 and 10 to fit with other Liberty ships.: