On the AC: the Vintage Air system uses the same unit for AC and heat so please look at the additional Vinatge Air paper I put in the manual pack for you. It will show the position that the knobs MUST be in for it to work. Essentially the heat must be all the way off, other wise the system is calling for heat and AC at the same time. Those knobs are VERY stiff so make sure the heat is actually off (vintage air says this was normal for their new knobs). Especially on the heat knob... there is a "hump" when turning it and that could easily be mistaken for the stopping point, but it is still on. Once it gets past that "hump" it turns easy again. This is very important, otherwise the evaporator is trying to heat and cool at the same time and your head pressure will be through the roof and cause the motor to stall. You also have an idle control solenoid that is set to run with coolant or air temperatures below a certain point, as well as when the AC clutch is kicked in, and it kept the motor at a smooth 900RPM with the AC running during all my test drives, so I am really leaning towards the high head pressure...
The through the hood spyder gas cap is vented by design. My guess would be that fuel sloshed around in transit and maybe even got on the carpet via the vent, or the S Florida heat is doing exactly what Charles described. If it is the vent I can walk you through closing that up if needed.
On the front trunk this is a common adjustment, but I am very surprised on your car because I must have opened and shut it 100 times and it was an extremely smooth latch. So, make sure you have it almost closed, with the safety in its hole, and with the heel of your hand push very firm right in the area of your hood crest emblem. Like Alan mentioned, make sure the release handle is also returned to :rest" and I would also just double check that the tool bag is above the tire, between the spare and the tank. If it sits any higher it may stop the hood from closing.
I'll resend all of this in an e-mail, and feel free to call if you need more help with anything.