I don't really think it's the trans... It sounds like you're bogging down and / or have a misfire.
So first a few questions:
Do you have a CEL
Are you having any issues at idle?
What previous issue prompted the fuel filter / pump change?
Is the hesitation affected by accelerating faster or slower, or does it crap out regardless of how much gas you apply?
When is the last time you checked your spark plugs?