I want to use pari and gap functions in Mathematica through WSTP.
The wstp.h ( from WSTP ) header uses a Microsoft MSVC specific __int64 type. So I must use the Microsoft Compiler. The pari headers however are written for the gcc compiler. The same is true for Gap.
No, that is not necessary. Mingw has an appropriate definition for the __int64 type in the _mingw.h header file, which is included from a number of other standard headers. For example you could do