any ideas, thanks. would it be the ypipe?

I'm not sure I understand your post Subject line. I think it means your car failed the smog test because it did not meet the standard for Oxides of Nitrogen. This component of automotive emissions is usually abbreviated NOX.

Modern car designs use two strategies to to reduce NOX.

1) Avoid creating NOX.
This is the job of the Exhaust Gas Recirculation valve.

2) Convert the NOX to less harmful chemicals.
This is the job of the Catalytic Converters.

Installing a Y-pipe probably eliminated two small "pre-Cats", and that hurts you at smog test time. However, other cars with Y-pipes pass the test. That makes me believe that if your EGR and main Cat are in tip-top shape, you will pass the test.

Limit was 3.00 I scored something like 4.75.... Other cars with similar size engines like a Buick Century got maybe 1.2 or something like that, not sure, but not as much as me. I scored fairly high on other things, like Carbon Monoxide levels as well, but good enough to pass, still failed for NOx though... I am not sure why it's like that, but my fuel economy is around 12 mpg, and it has been that way for a while. Other problems are hesitation, poor acceleration and powerloss. I'm suspecting the Catalytic converter as well, but I heard somewhere that I need to find the problem before or right after I replace the CAT, because CATs don't usually fail just like that, I did a small tune up, sparks, fuel and air filter and o2 sensor but nothing helped, ECU does not detect a thing, I've ran basic tests on MAF sensor, coolant temp sensor, and a few other things, everything is ok, but my fuel pressure does not drop as it is supposed to when engine is on, I ordered a new Fuel pressure regulator, then I'll probably get a new Catalytic Converter and see if it changes anything. I heard if the problem is not fixed, the cat might go again in sometime after I replace it.
And my car has no performance mods at all.
How is your fuel economy? Any changes or problems in throttle response? Catalytic converters can cause a powerloss, I am also suspecting fuel injectors, which would really suck ($$$$)