The way I see the master cylinder issue is you've got the following choices:
1/ Build it like Con did on NG's car and set the engine forward enough to clear the MC. Note this car has a cable clutch. Also note it is a Mk1 engine with the offset plenum on the inlet manifold that puts the throttle body closer to the centre of the car. Maybe you want the engine further back to give more room for a hairdryer at the front?
2/ Do similar to the above but get a Cultus inlet manifold and modify it so the throttle body is on the other (gearbox) end. This is a common mod to a Cultus manifold for 1300cc off road racers. Added benefit, more grunt. See this guy for a manifold:
http://www.redlinegti.com/forum/viewtop ... =3&t=49020
3/ Fabricate a custom intake manifold that avoids the MCs. See this part for a starter that makes the oval to round transition easy:
http://www.redlinegti.com/forum/viewtop ... =3&t=48587
4/ Modify your pedal box so that the master cylinders are above the parcel shelf inside the car. Or buy one of those top-hung ones posted earlier and use that. I would avoid the floor-mounted option.
5/ Get a left hand drive Rover pedal box. You'll find they have a torque tube that runs across the car then actuates an MC on the RHD side. If you can mix and match parts with a standard pedal box (and maybe fabricate a part or two) you could make this arrange ment have the MCs on the passenger side. Disclaimer, I want to investigate this but have never laid eyes on one of these pedal boxes, just something I've noticed on Yahoo Japan LHD cars.
Edit:
6/ Push the pedal box bacl 100mm like this one: (note it has the Cultus manifold with the TB end swap.)
M