It is possible to use -stim_files with 0/1 files correctly, but it is not easy. It is better to use make_stim_times.py to convert the 0/1 files to timing files.

If you want a fixed shape HRF, then 'BLOCK(d,1)' is a good starting choice, where the number d is replaced by the duration of the stimulus (in seconds).

If you want a variable shape HRF (also known as a FIR model), you can use 'TENT(d,n)' or 'TENTzero(d,n)' as the model function, where now d=expected duration of BOLD response (typically the stimulus duration + 12 seconds), and n=number of parameters in the model (typically one every 2 s or so, so n=1+d/2 is reasonable).

AFNI gives you a lot of control over your analysis, and the price you pay for that is you have to understand the options to be able to make an intelligent choice.

I strongly encourage you to do the analysis with afni_proc.py and let it set up all the pre-processing and analysis. It will (1) make your life easier, and (2) make it easier for us to help you.