Car: 98 Civic CX hatch
Engine: 2000 B16A2
ECU: PCT (Civic Type R)

The only mods I have are Intake and Exhaust. I've used the stock ECU and a JDM Integra R ECU with no issues. At startup it seems to lack fuel for about 5 seconds or so and then the ECU compensates and it idles normally. When the car is warmed up it starts just fine. There is no other issues other than initial cold start.
I've already checked CTS, spark plugs can't be the issue, or the injectors. Any help would be great.

 

Change your fuel filter.

 

Fuel Filter??? Not likely. That problem would manifest itself at all operating temperatures, especially during high fuel demand situations like wide open throttle.

I would suspect the pump not pressurizing the fuel system when the key is first turned to "run", or a faulty fuel pressure regulator. Or it could be a sensor that is out of range but not so far as to trigger a CEL.

To the OP:
Could you elaborate on the symptoms a little bit? Do you need to apply throttle during those 5 seconds or is the engine just rough during that time?

 

If I dont throttle it, sometimes it will die. Other times it just putts a little then idles at normal.