Not the OP, but my country runs a similar system. Each election station counts the ballots by hand. Anyone can signup for counting and/or watch the counting. It's mostly reps from all participating parties. Sometimes few independent citizens show up as well. After all people in the station agree on their total count (they can recount if needed), they phone in their numbers to the central station.

Raw numbers of each station are available publicly. The people who did the counting can check if their numbers were transmitted correctly. Parties usually have preliminary results from their people at stations way before the centralised system processes & publicises them. They'd easily spot any issues. Paper ballots are stored in secured bags and can be recounted if there is a need.