My '95 4.6 Cougar does the same thing. Shifts WAY harder on the 1-2 when done manually. Must be something to do with the 2 on the shifter really being 2nd (not 1st then shifting to 2nd like most cars).
Although, I've read on the TCCoA that the 1-2 accumulator on the older 4R70W's is designed with o-rings to seal it. Apparently, over time, the o-rings leak and it shifts funny from 1-2. The fix is to use the new style moulded rubber accumulator piston and the new spring.
Check out the tech articles on TCCoA under transmission. I'm planning on upgrading the accumulator in mine soon since it's cheap and only requires the pan be removed. (no f'ing with the valve body).
Regards,
Steve