You are probably fine to continue. It depends on the type of errors. A common issue with Family Tree Maker is that it exports a lot of things that are not allowed in the GEDCOM standard. They get most important things right. I would have to see sample of errors and warnings to see the issues. My guess is a lot of the errors are the same type of error. GEDitCOM II can continue fines even with those errors and warnings.
You may want to someday clean up the data to eliminate them. That task could be a challenging with 60,000 names. Sometimes, however, the fix is easy. For example, the validation step can automatically delete unknown custom tags. If you see lots of errors about GEDCOM tags starting in an underscore, then you can delete them all at once.