OK, it looks like you're having problems because the master cylinder is too long and is fouling the inlet plenum. I didn't have a problem like this with my engine conversion, the plenum is on the other side with a 2JZ. I had to mount my master cylinder on an angle to get enough side clearance (it was fouling the turbo), but that's different to what's happening here.
All I can suggest is scouring the wreckers for a car with a shorter master cylinder, there's bound to be something out there.
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