Hello,
You are right, if you use the harmonic constants coming from Oregon State University such as the TPXO global solution by activating the keyword OPTION FOR TIDAL BOUNDARY CONDITIONS, every liquid boundary with boundary code like 5 4 4, 5 6 6 or 4 6 6, are treated as if you want to prescribe tidal boundary conditions. Your case, with a river boundary, was not taken into account with this automatic calculation of boundary conditions for tide.
Nevertheless, can you tell me if you only have to prescribe water elevation for your upstream boundary which global nodes are number 9, 1985, 1986, 1987, 1988, 10 (last column with number 1797 to 1802)?
If yes, you can try the FORTRAN FILE for your specific case: tidal_model_t2_for_OGourgue.f
Hope this helps,
Chi-Tuan