Dear Bob. I just wanted to add that I really tought that at the end of Hulk, when Tony Starks goes to talk to the general, he's talking about the project captain america drug, and not the project hulk drug.
I also think that when the general talks to the guy who turns into abomination about the drug, he's actually talking about 2 different drugs. He reminices on an old one that showed promise (captain america) but then gives him a different one, not linked to the first one, made with the few info they had on how the first hulk came to be, which could explain the fact that abomination appeared, using an alpha project and all ^_^
That said, if you remember one of the animated movies of the avengers, Hulk is actually the villain. In that idea, it would make sense to say that there are two drugs, one for cap and one for hulk, and that tony starks wants info on the cap drug, not the other one.
And I totally agree on his father having worked on the stuff during WWII and Tony might even be there, as an infant. There is also a time lapse in the first Iron Man, where they say that Tony went under the radar between his father's death and his ascension to power at adulthood, which could be linked to the whole thing. Maybe. ^_^