It would seem that the new payroll system would never have worked manually either. Spotting that before anyone puts mouse to desk is the trick (and the greater part of Ollie's talk that day).
And it does make me wonder why not write a payroll system mainly from scratch?
Use an existing database platform, and write an application that mimics your manual payroll system.
The complexity of the system is usually much lower when rolling your own rather than customizing or munging an "Enterprise!" solution to try to fit your need.