You will not get the PX600 Pipercross filter in there with the brake master cylinder in the engine bay, regardless of what you do. Trust me, I spent well over $2,000 trying to get one of the things to fit with new carbs, manifold, reservoirs and ended up using K&N.
You may be able to use twin's if you drop the booster down but I think your filter options won't include a PX600