Hi Ipul
I went thru all you a going thru now. I did my swap back in 2009. from 1.34EFE m/t to BT.
Cat con remove by exhaust shop when change mid box before swap that time dono about it.
Same problem like sumbat, why because piping 1.6" for 1.3cc at first changed to 2.0" muffler use standard levin 20v,it improved the drivability.
but want to improve somemore, change to wheel to 14" 185/60/14 to 15" 195/55/15not much diff,
Change K&N filter, got better response, still not as good as 1.3 4EFE.
Than change fuel pump , now It seemed better response and nomore sumbat feeling. But felt engine very harsh and torque.
So get adjustable fuel pressure regulator set at 40psi(3bar) ,now feel the power comes more smooth.
but after two days become harsh, didnt no why, tought because of piping so go and change it at exss.
Than adjust ignition timing, vola..problem solved.
Each time change something I reset the ECU.
i takes at least 3days to get the optimum mapping.
Just do step by step dont rush, dono just ask. good luck.