As you have suggested, you have correctly created the tables and setup validation prior to importing the data files. This is the best way to validate the data on import.
The only way to import the data into your new files is:
1. firstly import the datafiles to new tables
2. create APPEND queries to add the data to the newly created tables.
Doing this you can create GROUPBY/TOTALS Queries to overcome any duplication and correctly Normalise the data.