Did you do a ssytem relearn when you installed the ecu ?
It probly wasnt working if you didnt....
If I was you I wouldnt take the trans apart just yet.
I would take it to a trans shop(or the stealership) and have it properly diagnosed.
Chances are you take it all apart, and its not the problem then you'll have wasted a day or two plus more money and still have the same issues.
Good Luck
and thankx for that link to the trans diag