In my opinion....
The master cylinder that has a larger diameter port should go to the front brakes (this is new information I didn't have before). The reason being is the larger port will deliver more brake fluid, faster then a smaller port will. Generally (there is that word again) you want the front brakes to apply faster then the rear brakes because the front brakes generally have more stopping power in most vehicles. If the rear brakes grab before the front, there is a better chance to loose control. If both ports (and both reservoirs) are the same size, I'd go with port closest to the pedal application end of the master, because it will be moving the fluid first, most of the time.
The word "generally" is used because it applies to brake function most of the time, but there are master cylinders that were designed for specific vehicles that have different requirements. If someone from P & J told you which port on the master cylinder to connect to the front brakes, I would go with what he said, he knows what he sold you. (I did tell you to follow any instructions that came with the master or the proportioning valve).
As far as that front brake line, I would add some support. Why would you want that long of a line to be able to freely bounce around without support and take a chance of it work hardening and possibly break? I don't know that it needs a full length bracket unless there is not another option, I would probably support it near the "S" shape or towards the center (the most likely location to bounce on that line) with a small bracket bolted to the frame (maybe one of the bolts under the radiator?) just to hold it in its position in relationship with the chassis without being able to bounce freely.
