CRX Fuel Surge problem when Driveing

[90CivicEx]

Ok so many of you know the crx has been down for quite some time and only come's out very rarely at the moment.

So the crx got it's first header on it last night and well the after market has 1 o2 sensor spot but the stocker has 2 o2 sensor spots. Well no check engine light is appearing and it runs great when stomped but The secondary I think is making the car surge when driven at a steady idle, but if I give it a tad more gas it goes away. Now my ecu is chipped and I understand I have to get the secondary o2 taken out of the program when I get it redone but before I go doing that could this be the problem of why it's surgeing a bit?

Just figured I would get a few opinions before I go testing theory's this time.