Hello and welcome to a problem I can't work out.

The pertinents:
EJ6 coupe automatic (i believe a B4RA) odometer is around 130k (but I swapped for an ex with a tach)

Only thing that isn't stock is the hood latch lever and the cluster.
I've put the last 40k on this car, kept up with maintenance and repairs as needed.
Did I mention the lack of rust? Body is mostly straight - the "damage" is only noticeable if I point it out.
BUT

The transmission has been the bane of my existence.
It has a mild "jolt" from 2nd to 3rd. It feels like it was hanging up or forgets it should shift.
1st to 2nd feels smooth
3rd to 4th mostly smooth
come to a stop sign or light from any speed and the transmisson "jolts" when you give acceleration.
Nothing has broke, nothing has changed these symptoms. I've even had the car in triple digits.
Years have passed at this point and I am just tired of the "jolt" 2nd 2nd 2nd oh look 3rd.
I have wayyy too many aftermarket parts sitting in the corner waiting to be put on
but I want to swap to manual because I can't afford a $10K complete kswap -_-
BUT maybe there is life left in this little B4RA, and I am just doing something wrong.
I don't race this car, I don't need 500whp (not saying it isn't cool just not my vision for this car)
And I already know someone is gonna say "why did you buy the aftermarket parts instead of the swap".
Because 500 here and there over the course of 5 years is WAY cheaper than 10k all at one time.
Sorry for the rant, Not sure what I should or could do. Open to suggestion
Thank you in advance for taking time to help me with this

 

If I do try to swap to manual, is it a s40? Sorry if I am full of dumb questions :s