Quite a bit of a puzzle, that, leading the players in an investigation without losing them. I've played my share of purely investigative games, and my best advice would be to be very flexible in your scenarios. It's a virtual certainty that your players will miss some clues, invent some you didn't think of, and/or jump over other and still end up in the right place, so your best bet is to forget about anticipating them entirely. Write up your protagonists, and write them up well, so you can have them react appropriately to what your players do. Make a very detailed timeline of everything that happens, so that you'll know what is happening wherever it is your players end up at. And then just cut them loose, and be prepared to improvise.
If you really want them to follow a series of clues, perhaps the best way is to make your clues people: talking with the witness A will give them the name of B, who will give them C, who will lead to D. People are flexible, so you can adjust their responses to make sure the PC do get the name that matters, and names are names, it's hard to misinterpret them completely. Whereas there's not telling just how far a group of imaginative PCs can end up on the basis of a button or some cigarette ash.
And prepare a plan B, something like a NPC with a big neon sign screaming 'Here is the villain' (figuratively speaking) that you can trot out if all else fails.
