As you may know, the function of the R terminal is to supply a full 12V to the coil while cranking. The coil normally runs at 8V or so on a stock set up, so the R gives a little extra to get the car started easier and it drops out when not cranking. Your new petronix won't need it. In fact you should remove the old resistor / ballast set up and give the coil a full 12V when the key is on.
I dont see why you need the Ford solenoid in the trunk. You could keep everything stock and just run a longer battery cable to the trunk battery along with your 8 gauge from the battery to the horn relay block. just my .02.