Can't speak to the ease/difficulty of the R&R on a '66 C body heater box. If there's A/C involved, it's harder than without (duh).

I can speak to the bypassed heater core question:

You not be alone by any stretch of the imagination of you looped a length of heater hose from one outlet nipple back into the other at the engine. No harm whatsoever to buy you some time.