Start with the counts, not the rows. Separate exact matches, rows within tolerance, rows over tolerance, rows with no tolerance, and rows that could not be paired because the employee or pay code had no mapping. Clear the mapping gaps first: they are comparison problems, and they distort every other number.
Next, group over-tolerance rows by category and pay code. A single configuration error usually shows up as the same pay code differing for many employees, so one fix can clear dozens of rows. Differences spread across many codes for one employee usually point to that employee’s data: a missing rate change, a different work location, or an input that reached only one system.
Look at the direction and the components. A consistent sign suggests a rule difference; mixed signs suggest timing or input differences. Where you have number and rate, check which one moved.
Review net pay last. It is what employees notice, but it is the sum of everything above it.
Finally, track the over-tolerance count across runs. If it rises after a fix, the fix moved the problem rather than solving it.