Yes, I used both in a side-by-side evaluation for three months while I was evaluating which to buy.
The biggest difference that I noticed (other than the results being slightly different) was in the functionality. NE/NASTRAN does not support all of the same cards found in MSC/NASTRAN.
However, I believe both are capable of exporting results to a neutral file format which should be able to be read by either pre/post processors. As far as sharing model files, I suggest writing out the input deck and importing directly into FEMAP and/or PATRAN. Once imported, the pre/post processors will warn you of which cards it is having problems with at which point they will need to be edited.
Hombre
P.S.
How do you like NE/NASTRAN with FEMAP? I ultimately chose MSC because of functionality and my preference for PATRAN.