Is it possible to just remove the heater control boxes, air guide plates, air ducts/elbows, J-pipes, etc. without removing the SSI heat exchangers....or is it just easier to remove everything? I'd like to clean up and repaint all of these items when I repaint my new (old) banana muffler.

they can be removed without disturbing the heat eaxchangers

don't lose the hardware for the control boxes. special nuts and bolts hold them tight to the HE, and the control cable has a special attachment, like your accel cable.

some stuff inside the engine bay needs to be removed to get to some sheet metal screws. At least on mine I have to remove the L-jet air box, then the aux fan. But I have had mine off several times.