Wonder if running it dry could let a piece of debris flow down, scoring the piston bore wall or nicking a seal.
BTW, the Marlin 'Big Bore' MC is the stock Aisin FJ80 Non-ABS part, it's 'big' relative to the standard size Hilux. The FJ80 came with a 1" piston, which would upgrade a '79-'85 mini truck that came with a 13/16" piston. The potential upgrade for you would be to a 1-1/16" unit from a HD T100. But doing this with no other changes (primarily using the matching booster) might make the pedal even more mushy. BTW, I don't know if the FZJ80 has a different MC and I'm not sure how ABS affects your swap options.
I once went through trying to figure all that out. My truck was delivered with the 'big' bore master cylinder (what some people call the 'V6' brakes). The engine in the Hilux does not seemed to have been the determiner of what brakes you got, but rather if you have 8" or 10" rear drums (1986-1988 IFS I think had 8" but all trucks from 1989-1995 have 10" rear drums) and the caliper piston size. In any case with a FZJ80 you would already have at least a 1" bore master cylinder and maybe a 1-1/6" since some 4Runners (V6 from 1992-1995) and many T100 had them.