Ok, so after spending a few hours jerking around with plate leveling, this is what I found works best for aligning the two heads.
1 - Level build plate to one head left or right it doesn't matter
2 - Disassemble the other head (non-leveled) and remove drive motor that you did not use for leveling
3 - Center the heads to the middle of the build plate
4 - Loosen the set screw for the head that you did NOT level
5 - Use a piece of glass and place it under the heads and manually raise the bed by hand via the center screw until the glass makes contact with the head you leveled
6 - Set the height for the head that you did not level with. Set the set screw lightly.
7 - Slide the plate left and right off the heads to make sure the plate can go between BOTH heads with the same resistance. Repeat #5 and #6 as needed until you are satisfied with the alignment
8 - Tighten set screw for the newly aligned 2nd head
9 - Re-assemble the drive motor
IMHO, this is the best procedure to align both heads to the same height relative to the build plate level. Now the factory build plate isn't the highest quality and I'll probably be upgrading that to one that is even more flat.
This may work if the nozzles are within .0005" of each other, but the gearhead change you are describing only opens or closed the upper end gap about .003" maximum. at minimums, you need to shim the distance from the hot end's base plate to the cradle for .001-.003", after that, you need to tighten the nozzles to same heights.