The rectifier tubes aren't assigned to a certain pair of power tubes. Being wired in parallel, they share the load. You don't even have to remove one if you're using the diodes, or if you want a stiffer tone. Mesa recommends removing one to keep the same amount of sag as all 4 power tubes would have when using the tube rectifier.
Also, when removing power tubes, just make sure you remove either the innermost pair, or the outermost pair, and not the 2 to the left or right, and plug your cab into the output jack that is half of the cab's impedance to keep the same frequency response. If you have an 8 ohm cab, then use the 4 ohm jack.