So mostly it is the non-extruding nozzle that is dragging across and squishing the top of your print?...Gonna go out on a limb here as I do not own an Apprentice, but I am building my own dual extruder mount…so here goes:
Although it is critical that both nozzles touch the bed at the same time, the bed must still be as parallel with the entire X movement as possible. Otherwise, even if both nozzles are parallel to the bed at, say the bed center, then once the carriage moves in the X axis, the gaps would increase or decrease.
Now, while the auto-leveling routine should compensate for this by adjusting the Z movement during the print, it may get slightly out of whack with respect to one nozzle or the other.
My advice would be to take something that is a bit longer than the distance between your X carriage rods and the bed while the nozzles are not touching it; then use that to get the bed as parallel to the rods in the X axis as possible using the wing nuts.
Then, bring the bed up to the lowest nozzle, and adjust both nozzles so they touch the bed equally.
Now adjust the bed in the Y AXIS ONLY to get that correct to the nozzles.
You would still need to adjust the Z stop (probe) to home Z properly as well and not crash the nozzles into the bed; but at that point, both nozzles should be parallel and equidistant to the bed as possible in all bed positions.
Again, I do not own an Apprentice, so take this advice with a grain of salt, but this is the route I would take to minimize any mechanical issues…
SD2 - Stock - Enclosure - Heated Bed - Glass Plate - Auto Fire Extinguisher
Ord Bot Hadron - RAMPS 1.4 - Bulldog XL - E3D v6 - 10" x 10" PCB Heated Build w/SSR - Glass Plate
Thanks for All of Your Help!