So finally now I'm driving my car and there's a huge change in the performance after the engine work and the setup.
However I couldn't get the P2J-003 ecu to work and it was only because of the 3 wire/2 wire conversion and intake manifold difference.
3 wire IACV Auto IM (with EGR)
2 wire IACV regular IM (no egr)
So the problem was when I was connecting the P2J-003 ecu it kept looking for the 2 wire IACV and my car had the 3 wire IACV Auto IM. So I gave up on the P2J-003 Ecu since my car was working fine with P2J-J63 ecu. Didn't throw any CEL and no codes.
Tested the car and works fine as it should with this setup. I feel a slight bog and hesitation though below 2500-2800rpms which i think is definitely due to the lean burn but once it crosses that mark I can feel the difference in the throttle response. And also I'm averaging over 11km/L these days with no AC. Will post and update more once I refuel and get another reading for an average.
Not sure if I might sell my or keep the P2J-003 ecu for later if i ever decide to go without an EGR and install 2 wire IACV IM to see a better throttle response, as I've heard that EGR doesn't help with the economy and also the hesitance below 2800rpms isn't there which results in a better throttle response.
Last but not the least I'd like to thank u all once again for the help. I'll try to post some more pictures and videos to help anyone else who wants to get this setup as it fulfills my expectations for a daily driven sedan with 130hp. Good average with light foot and a bit of performance if you want to full pedal or floor it.