I had similar symptoms, but with a turbo. Turns out that the turbo compressed air feed into the intake manifold was loose and leaky. Point here is that the problem isn't necessarily in the tranny - could be the engine. BTW the hard shifting I had was 1-2.

__________________
JSR

1983 300D Turbo
1995 E320 Wagon
2001 MR2 Spyder
2001 Subura WRX Sedan