Oops, sorry about forgetting to label the ventilation. I'll double-check next time. Anyway, my suggestions:
On the room layout: I'd at least consider Security room A2/B2, Medbay A3, R&D A4, Small Quarters B4. That'd give an even longer channel for intruders from the Warpgate (we can build into B3 later, connecting only to the Control Room), although we've probably lost anyway if the security room falls and general ease of movement through the facility may be hampered.
On the crisis situation: +1 to escaped lurker's Option A. If the aliens seem friendly enough, we might want to consider collecting some air & soil samples as planned, activities which should make it pretty obvious that our main purpose here is peaceful research. Maybe even signal a desire to swap one of our rifles for one of their weapons? Otherwise just hightail it if the team leader decides the situation is too hazardous.
On specialists: Just as a note, the specialist wages are listed as weekly, so with four weeks between budgets that's a fifth of our income gone if we get all five. (if they take up barracks slots we can only hire four at the moment anyway.) I'd suggest hiring Dawson, Stevens and at least one of the others, though I really don't mind. Speaking of income, the footage from this encounter should make for a convincing argument for more funding regardless of how it goes.