The Connection to Howard

I never thought that there was enough explanation for how Scott was so sure that Howard was in on the whole thing. I can conclude fairly easily how Scott could have assumed that Howard was a part of the whole thing, but how he made the absolute certainty always confused me.

I imagine when he was investigating Zack Gregory, and came to find out that a lot of the information he'd already been given wasn't given to him in a formal and professional matter, when Howard told him that it was, that he probably placed the connection there.

Or it could have been when he finally caught Gregory, and Gregory told him that Boyett was not in charge of the whole scheme. Scott cold have then concluded that it needed to be someone with power and an ability to hide things, and maybe he concluded Howard through deductive reasoning.

However, the movie really didn't show him making the connection there, and then when Scott confronts Howard at the warehouse it just seems sort of out of left field to me.

Is there something that I missed? I just can't seem to put my finger on how Scott was able to put two and two together and know for a fact that Howard was the head of the operation.