The digital caliper is a great tool that no self respecting home tinkerer should be without.
A simple technique allows accurate hole center to center measurements.
First set caliper to measure the hole diameter, but instead of reading the diameter, zero the caliper.
Now the hole diameter will be subtracted from any subsequent readings. Use the caliper to read the outer edge to outer edge of the two holes you want to measure, and the hole diameter will be subtracted from the measurement yielding the true center to center distance.