I agree with what Gandolf has outlined here with emphasis on the same very particular points he made.
I use a program called Relatively Yours which is quite versatile.
Since I have not yet installed my latest version (into which I plan to manually enter everything for a number of reasons) I will refer back to the original DOS version of the program.
The DOS version had a couple of extra packages available and one of these included a facility to do pretty much what you want.
You can either Import or Export data in GEDCOM Format and this program has a structured checklist to fill out so that the Imported file will be taylored to your own needs.
Basically it is as follows:
What is the name of the GEDCOM transaction file?
What are to be included on the Translation Log?
(A=all entries, N=no entries, E=errors only)
Record the reference numbers from GEDCOM input?
(Y=record as reference material, N=ignore)
Create CODE or AGCI format records if possible?
(Y=CODE or AGCI if input suitable, N=FREE format)
Concatenate NOTES if longer than 70 characters?
(Y=yes, N=no)
Convert all input or selected persons only?
(A=convert all, S=select individuals)
In what format are numeric dates (if any)?
(1=ddmmyyyy, 2=mmddyyyy, 3=yyyymmdd)
Date stamp records added with today's date?
(Y=yes, N preserves input dates of change)
Allow manual intervention for dates before 1600?
(Y=yes, N=no)
Permit termination if excessive inconsistancies?
There are no doubt further fields to deal with but I have stopped here otherwise I would have to specify a legitimate file at question one to proceed to the next page.
However, the basis for an answer is here.
Another facility in this program is to "MATCH NAMES against a file from an outside source"
Basically what you need is an import medium that supplies as many data checks as possible and also a great deal of care.
Hope that is of some help.