So if I swapped the new CPU in, could I go about doing a regular jtag on the box?
Assuming the CPU is old enough that it hasn't had the update applied and the CPU matches the board revision, then yes.
What Frappe051 said is more or less correct.
If you didn't have the CPU key already, you could always just boot XELL after you transplant to cpu.
*Replace non-exploitable CPU with exploitable one.
*Install JTAG/SMC wiring.
*Run XELL to get CPU key.
*Build and flash new freeboot image to NAND.