I'll try to help you out before vanishing (again) for a few days. I promise I don't take a week off after answering each question post.

We're in the middle of moving into a new home and office during a darned heat wave! It's supposed to be above 105f the entire time we're moving - how's that for timing?

Okay, whining aside, let's get to your questions!
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1. Are AT4 (and similar weapons) one-shot (in the game)? I searched through the forums, and people have discussed a TQ roll for every shot after the first, but I would like to hear other opinions.
It's really up to the scenario. Some scenarios will dictate how many shoulder launched rockets/missiles a unit has for the course of the game. In those that don't, have the unit declare it's going to fire a missile and make a TQ test. If it passes, it has a missile ready to fire. If not, it can't fire because they didn't get the missile prepared right, they had to get a spare missile passed down to the shooter, etc.
We do it this way not just to avoid book-keeping, but also because soldiers will carry a lot more stuff with them than their paper equipment charts show. If you've read many of the first person accounts you'll find references to non AT team guys carrying spare missiles or about teams shooting tons of SMAWs or AT4s. In Fallujah, particularly, everyone pretty much went loaded for bear.
You can certainly decide on a cap for how many missiles a given unit can carry yourselves, though!
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2. When rolling D6 troops vs D8 troops, obviously you cant beat rolls of 7/8 so no need to bother rolling against 'em, right?
That's true - but we usually have the attacker and defender roll at the same time and then match up dice.
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3. "In Cover" - USMC squad behind a wall gets shot at with 5 FP dice gets how many defensive die?
+4 (number of figures, which is < than FP)
+1 cover (behind wall)
+1 ("In Cover" because they are behind cover - if they were Exposed they would roll TQ to try to get "In Cover")
+1 Light armor
Defensive Die = 7
Is this right? "In Cover" was the thing that confused us the most.
In Cover does confuse some people In Cover means that rather than just being behind a wall, the unit has had time (or has the skill) to "hunker down" into firing positions that give them the best possible protection. It's the difference between just standing anywhere behind a car to shoot and crouching behind the engine block and/or being prone shooting around the wheels.
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4. Buildings - there is no distinction between being "in" a building, or "on top" of a building - right?
We had a lot of terrain, but it felt like we were playing on a flat table since most units were on tops of buildings and so could effectively see one another.
Are there any blind spots or anything?
Units in buildings have 360 degree LOS - but that doesn't mean that intervening buildings and terrain don't block LOS.
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6. Any feedback on this scenario?
It is clear that the insurgents cannot trade bullets with better quality troops, so I imagine that the answer lies in local superiority. By this I mean getting 4 units to shoot at 1 regular unit, so by the time the 4 unit fires then the return fire is (hopefully) less lethal. But, this method will still leave your units hurting so I don't know how well it will work long term.
I effectively felt like I couldn't do much without getting my ass shot off.
You describe a useful tactic. I'd suggest you revisit Capt. Jake's excellent TTP section in the back of the main rulebook for tips, too. One thing that Insurgent players forfet sometimes is that Reaction Fire doesn't just cost Regulars FP dice, it also costs them MOVEMENT. In a scenario that requires them accomplish tasks within a time limit (which describes pretty much all of our scenarios), you can really bog Regulars down with fire - even if it costs you every unit that fires. After all, you'll get more cannon fodder from reinforcements.
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7. Lastly, setting up terrain. Per the map for the scenario, its a dense urban area (duh, Fellujha) but we had trouble matching the number of huts even though we have (what we think) are appropriately sized 20mm huts. Any suggestions on translating the maps to the table? We have considered building new huts that are smaller, but im afriad they might look weird compared to the figs.
Don't get to hung up on trying to exactly simulate the maps. The primary purpose of the maps is to give you an idea of terrain density, LOS blockage, and distances between units and objectives. Six huts on the table works just as well as 12 huts jammed into the same space, so don't lose any sleep about it!

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Oh and we loved the game =D Much less complicated to figure out reactions when you play through rather than trying to work it all in your head.
I'm tickled to death to hear you had fun and I think you're exactly right - the Reaction system is hard to explain in writing, but a breeze to play out on the table. I think it falls into place pretty easily when people take the time to just walk through it on the table. We need to get some online demonstrations posted up so people can see how simple it really is.
We'll be doing that in the NEW Stately AAG Towers once we get moved in.
