How have other DMs handled PCs with access to scent and the ability to magically read items during the initial investigation? Do you think that such abilities solve the mystery, or do they just give a major lead?
Scent was almost an issue with my group, luckily my PC rolled so poorly it didn't matter. As ideas it could lead them to the safe house where Skreed is staying so you can out as many or as few clues as needed. Or as an alchemist he could probably come up with a way to fool scent.
No idea about object reading or what you mean at low levels.
The biggest clue is the hopeknife and you want your PCs to discover it isn't his and should go to the smith to find out more.