The AEC does publish the totals for each candidate, at each stage of the Senate count [1]. There is a PDF for each state, under the heading "Distribution of Preferences". An example for NSW is at [2] Are these numbers sufficient input, to duplicate and verify the results of the AEC software?
Not really the same as the raw input, because while most people vote above the line, there will be a small number who vote below the line, and the incremental count doesn't show if these were allocated correctly.
The best you could do is compare the expected flow each step, based on group voting ticket, against the actual flow, and make sure the total difference does not exceed the number of below the line votes.
Do they publish how many people vote below the line?
Edit: Antony green has an estimate used in his calculator.
"At Federal election, around 95% of mainland voters, and 80% of Tasmanian voters, fill in their ballot paper using the group ticket ('above the line') voting option."
As I understand it - yes normally these numbers are sufficient to verify outcomes.
However in extremely close races, such as what happened in WA - it can come down to very small numbers of individual ballots and how their preferences are stated, as to what order senators are elected in.
The best you could do is compare the expected flow each step, based on group voting ticket, against the actual flow, and make sure the total difference does not exceed the number of below the line votes.