The 3/4 lever being positioned down is because of the way they changed things around to achieve the overdrive setup. The OEM overdrive gear set used what was 4th gear for 3rd and 3rd became the 4th gear which was cut to be less than 1:1, so overdrive. I understood this change in loading necessitated the larger input shaft bearing.

I don't believe that would affect the 1/2 shifting. If something was out of position 'up front' because of the lever being incorrect, that should affect your trying to go into 3rd. If it was badly out of position you'd be having problems all the time and even moving the shifter across the H pattern would be difficult, because you'd be fighting the detents in the side cover mechanism.

Jamie will be much smarter about this than I. Hope you get it sorted out.