Guys PKDM cars do not have secondary O2 sensor they have primary O2 Or AFR sensor. It is necessary to adjust your short term and Long term fuel trims. Well if you have not genuine harness then it may not get connected to scanner via your odb2 port. So you would be diagnosing problems by hit and trial
What engine you have got in there ? D series? if yes wiring is easily available here complete uncut wiring would cost you approximately 5-8k. I have seen many here.
Is your car manual or Automatic?
Seems like this car has been done by another Nito Tape Ustaad. I have one accord and i sorted it out each bit of it.
If you are getting CEL in regards to generic P700 transmission code then again your car would run like crap and wont rev beyond 4800-5k RPM. I think you are using Auto ECU. In this case your VTEC would not even kick in.