The simple answer is no. The complicated answer is yes.
The TCU could be left there.
The ECU would either have to be swapped for a manual TCU, or the complicated answer would be to convert the ECU to manual from Auto.
I haven't done the second option, but I know that details are on the PGMFI.org site. You can also ask that specific question in the ECU forum, or better yet, search for the answer in that forum before asking.
What was your original TCU? By this, I mean, what was your original engine?