When you upgrade the iron, the blue wire on the plate choke goes to pin 2 on the 4 pin socket, the black wire connects to the end of the power supply where the C-7X connected originally.
For wiring the secondaries, the manual will give you instructions for 4, 8, 16, and 32 Ohms. For what you're doing, these are now 2, 4, 8, and 16 Ohm hookups.
The wire from output transformer terminal 10 can go to ground, or to the center lug of the hum pot. The wire from output transformer terminal 5 needs to go on the output side of the parallel feed capacitor (the input side will be wired to pin 2 of the 4 pin socket, you want to connect the output transformer to the other side).
The leftover C-7X can be used in place of the 270 Ohm resistor in the power supply if you can find a proper place to mount it. My suggestion is to mount the output transformers underneath the chassis, and the chokes up top, especially if you wire the output transformer primary to the center leg of the hum pot.