The only concern that comes to my mind would be hydrogen sulfide, but it would have to be pretty concentrated to cause issues. If you start hitting some smelly, black sand then I'd perhaps slow down or do the process in parts. It depends how far in you are though. If you're 3/4 of the way done before you notice signs then you're probably fine to finish. Your nose will detect it at concentrations far lower than when it becomes a toxicity issue. It builds up from bacteria when you have anoxic zones without nitrate to process.
I also wouldn't worry about the blocks, but perhaps I'd have some slight separation (maybe 1 cm, give or take) between them for some water exchange. The more flow (i.e. oxygen) they receive the more nitrification they will perform. Less flow would promote more denitrification. They still need good access to nitrate to be effective at that though.