Justin:
The time you spend in setting up for measurement with the Protege will be recouped within the first one or two measurements that you can make without using the Jones, so it does not make sense to delay the switch. Besides if you wait too long the Protege may become unavailable and your only option may be the Jones.(The consulation will be that your time developing the spreadsheets will not have been wasted!)
I believe you and Pete are following the Measurement Manual and making final course adjustment by converting counts or revolutions to standard units such as meters and measuring with a steel rule. Recently in MN I described a much simpler and more elegant method that avoids this conversion and measurement with a steel rule.
For instance with a fixed start and variable finish, the measurer simply selects the line at the finish of the ride that gives the longest course as the certified finish. The only calculation (in cts or revs) necessary is that for the pecentage difference between the two course measurements using the cts or revs found during the second ride for the first finish. For a fixed start and finish the measurer simply adjusts the U-turn using bicycle measurement.
Note that, although not intuitively obvious to most measurers, the above course adjustments in cts or revs are valid even if there is a diffence in the second ride with the rider, bicycle, day, or temperature.