DP and Sixto have good points. Make sure the vac modulator is holding vacuum and not leaking (test with MityVac). And if the IP is too lean, so you're using too much throttle to get 'normal' power delivery, the shifts will always be harsh. Conversely if you've removed the ALDA, you could get the opposite, some flaring due to too little throttle travel. It's odd that you have some flaring and some harsh shifts.
What fluid did you use when you changed fluid/filter (specifically, was it Dexron II/III spec, or Dexron VI?) and did you drain the torque converter to get ~99% of the old fluid out?
Could be a faulty vacuum modulator, after the items above, I'd probably replace that before considering a transmission replacement. Bummer you're not closer, I have a good used 87 300D trans collecting dust in my shop.
