I think it's obvious that the change to the fan/clutch is what's causing the issue. Unless I'm missing something here I don't see how a steel support bracket for motor mounts can be designed to work with normal operation of the drive train. Rubber mounts would be designed to work properly. If there's too much movement the mounts would be redesigned to work better. The only purpose I can see an additional steel bracket is for safety reasons during a crash, holding the drive train in place if rubber mounts break. Metal to metal or metal to rubber for extra support doesn't seem logical if you're trying to reduce movement.
If it were my car I'd try Don's modification first and reevaluate from there. EDIT: I see that you've done that already.
Just a long shot... Is that a standard height trans mount? My fan has slightly more clearance on the top of the radiator than it does the bottom, so maybe under braking the trans can lift slightly when the mount flexes but not change the angle of the fan enough to hit anything. It'd be fun to mount a camera next the fan and in the tunnel to watch to movement of the drive train.