I thought the ending was really good. Especially given the time constraints of a con game, you can't really beat yourself up if it turns out well. Look at Ross's infamous Age of Masks game (the player choice one). It is so rushed at the end its really sad. Your game had a perfectly executed, satisfying ending. The lead up to getting peopel to the reactor was a little railroady (You want to escape? Great, I'll tell you where the reactor is!) but after that the threat opf the Colonel and Grunwald's presence built the tension well. Grunwald was handled perfectly I thought - this very off, strange personality - whose voice even became a little more monsterous at the end - yet there was not one reference to ghouls in game, or his appearance (aside from glowing eyes, again at the end) nor explicit reference to 'I want to eat the bodies'. Just a wonderfully creepy unknown encounter, that in a normal campaign would be a great jumping off point.
I thought the start felt a little sluggish, I don't recall why the other play through with Ross, Bill and Cody went faster (could they just leave the truck?).
I think the amount of dice rolls asked for seemed excessive, I'm not sure where the tipping point with that was, there just seemed alot at the start. I think mostly idea rolls seemed too much, then again if you are trying to nudge players not coming up with ideas, I can see the temptation.
I thought the base stuff was well done (except for the small quest nudging at the end) and the combat with the weird creatures fun. It was nice to see aspects we haven't heard of before in Tom's released play throughs, like the soldiers in the barracks and like actually trying to get the vans going. Somehow Tom's games had a grander feel to the plot - I think because the players were pushed into the main plot from the word go. I think if the players in your game had only touched upon the plot as much as needed to escape with the plane or truck, it would have left it a mysterious and grand weirdness. Not sure exactly what was off on that, and it's only a minor thing.
The way the players were removed seemed fair - the horse was dangerous, and the player at the reactor did almost choose his own fate, and only bad luck saw his friend not aid him.
Anyway, an impressive first gencon GMing! Hope to hear more games in the future!