If the CA is setup to control the throttle of the controller, rather than directly running your throttle in, then it can take a while to tune the CA to ride the way you want it to.
If you don't want the CA to interfere with your throttle control, you can set throttle mode to PASS THRU or BYPASS; one of those modes directly sends the exact throttle input directly to the output with no limiting or modification, etc.
If you still have problems with the ride after that, it's not the CA's settings doing it, and would then probably be a connection or battery issue (since those should be the only other things changed given the parts you've changed/added).