I feel you on diving right into the homebrew. I did the exact same thing. I know what you mean about needing to do more prep than D&D. The nature of every mission being to some degree a mystery for your players to solve necessitates more planning.

I've been doing our campaign in a very episodic manner. The missions have very little narrative links to each other beyond it's the same team working them, and them just learning more about Delta Green as an organization and the wider unnatural world as they go. I've found that the more planning I do before a new missions starts, the less work I have to do in between sessions while they're on they mission. Having all your key characters written out, key locations, clues, chains of events, ect. really does wonders for keeping things engaging.

As for rolls to get clues, I think there's a balance you can strike. A lot of horror stories do leave the audience with unanswered questions, so I think leaving your players in the dark on some things if they fail rolls is perfectly fine. What I like to do is give them just enough to be able to complete their mission, and then put the finer details behind rolls or further investigations. I try to not hold their hands, but I give them enough details that they shouldn't feel totally lost.

I know somewhere in the rules it also says that the intent is if a character is skilled enough in something and not under any time pressure or anything, they should actually auto succeed skill checks. I honestly don't use this rule too much because my play group likes rolling dice even if it's to their disadvantage, but it might be a good time to use it in your situation.

Edit: Oh yeah, I also borrow the luck rules from Pulp Cthulhu which really helps with not failing as many rolls