Hi Brian,
It's not clear to me what you're trying to do. Mbed TLS supports Curve25519 arithmetic for X25519, accessible through the mbedtls_ecdh_xxx interface. If you want to use Curve25519 for some other purpose, this may or may not be supported via direct access to the mbedtls_ecp_xxx interface. The curve arithmetic code only supports predefined groups, it does not support changing the generator without patching the library.
For Curve25519, the generator is the point (X,Z)=(9,1). Isn't this the generator you want?
Best regards,