1. Is it hitting the master cylinder itself or the reservoir?? If it's the reservoir then you might need a setup like mine with remote mount reservoirs. If it is hitting the master cylinder then I might need to see a pic of the setup. My car was supercharged and is narrower across the engine bay than yours so it should fit. I won't recommend a different type of master cylinder though until I see what you already have.
2. No factory alternator bracket was acceptable on mine either, so mine runs a cutsom made one. Pretty easy to do, just make sure it is STRONG and properly aligned.
3. Assuming that you mean your old water line was just T'd into the heater line. Just block off or remove the T in the line so that your heater lines are returned to there original routing. If this is not right or unclear take a pic and advice will be more accurate.