I looked over your system and project files.
The export format was set for “Binary file (32 bit, int)”, not “Binary file (32 bit, float)”. This will likely cause miniDSP to see NaN when importing.
Regarding filtering, there was an 2nd order all-pass IIR at 38 Hz and a 2nd order maximum-phase all-pass on the “FIR Phase Adjust” tab but the tab’s “Enable” was unchecked. Try removing the IIR filter and checking the “Enable” on the “FIR Phase Adjust” tab. This should give you a FIR that unwraps the LF phase for the measurement in the project.