Thanks again for all the help.

Yes, we rebooted the server, rebuilt all of the indexes, and resampled the statistics. When we compared the execution plans between systems, they were identical. The data size is approximately the same, 3 million rows (since 2005). Now we are looking at configuration options.

When we remove all the functions the process runs is seconds, then as soon as we add just one back, we have extended run time.