Yes. Routing side A only with side A and side B only with side B is good. Merlin Blencowe even makes a good case for twisting each triodes wires together. I've never done that, but the point is to minimize any stray coupling.
The Ceriatone layout looks good. Just abandon those holes and make new ones. I understand it's getting crowded to put the tube sockets between the board and the back panel jacks. Just test fit everything a couple times. You could even remount the board closer to the controls since it looks like everything is wired up over there. The jcm800 is not as high-gain as a lot of amps, so you can get away with a lot. You can series string the heaters together as well.
One more thing: You will want your output level to be "stomp box level". Simplest way to do it would be to replace the 1M master-volume with a 470k dropping resistor to 50k potentiometer. Technically, that is not a low output impedance, but it is as good or better than a lot of stompboxes and simpler than building a buffered output/effects send circuit. It will drive a 10 foot cable without too much top end roll-off. Likely you will have this close to the power amp, so there will be no issues.