I don't see anything in the layout drawing that would create a ground loop. Unless you use an input jack that isn't insulated from the chassis AND you also connect the jack to the ground lug on the chassis. If you use an uninsulated jack just connect the board's ground to the jack and don't use the ground lug on the chassis.
You could split the grounds as you propose, though, and run the power grounds from the board and the power transformer to a separate lug on the chassis. That would provide a slightly lower resistance path to ground for them.
Yes, on the drawings C6 connects to both pins 3 and 4 on V2. It's for "heater elevation." The difference between the two heater wires will always be around 6 volts AC, but without being referenced to something the voltage is free to float to whatever level it wants with respect to ground.
Usually the heater winding on a transformer is a split one with the center tap connected to ground for a reference. In this case the winding is not split and the heaters are referenced to a positive voltage. The theory is the positive reference induces less hum. And for convenience, they chose to use the fixed cathode bias voltage for the output tube.
I built a version of this amp a few years ago. It started as a P1 but I eventually put in the rest of the parts and upgraded it to an SEL. I experimented with several references for the heaters, including using ground and a separate voltage divider connected to B+ for elevation. I ended up making an artificial center tap for the heater winding using a couple of 100-ohm resistors and connecting it to the output tube's cathode for a reference. I found this to be the quietest in terms of hum. Basically just connect one 100-ohm resistor between pins 3 and 4, and another 100-ohm resistor between pins 3 and 5.
snow rider 3dI haven't heard that the cathode capacitor on a power tube can affect the bias on preamp tubes. If it's bad it will definitely affect the power tube, of course. Also if the power supply isn't working right because of bad capacitors, the whole amp won't work right.