API to Report "Limit" not working as expected

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We're trying to export data from some large tables, like transactions.
 Basically the Object model doesn't work for dozens of reasons so we have to use the RunAnalyticsReport API call to call a report we've written in the application to retrieve the data.

Unfortunately we're running into major problems with some of the tables. For example, "Transactions"...

It doesn't have a unique Key or Single index for us to sort on.
We can sort on date, but that's not unique at all.
The API's row limit is 10,000
But we have no way to limit the report itself to 10,000 records because there is no unique id.