Unfortunately, there is not a method that will completely account for changes in the geographic definitions. We leave the ultimate decision of how to account for these inconsistencies to the researcher. Some researchers choose to ignore the changing definitions; others attempt to piece together the consistent components of METAREA as best as possible; and, others develop a unique method.
Regardless of what you choose, I do recommend comparing your final MSA-level data to published Census tables for the purpose of determining whether or not your results for a metro area will be biased by the changes. The NHGIS project, which is also housed in the Minnesota Population Center, offers many of the official Census tables going back to 1790 at several geographic levels, including metro area. While NHGIS is primarily focused on mapping data, the summary tables can be extracted independent of shape files as .csv files with optional descriptive headers. Additionally, the Census’ American FactFinder site is another source for Census tables.
Hope this helps.