No sense in replacing the O2 if the cat is gone.......

 

Then my question is, is the ECU running 'limp mode' because of the missing cat?

 

The car is not in limp mode. That second (downstream) O2 sensor measures the oxygen content in the exhaust once it is past the catalytic converter. The second O2 sensor does not factor into the air/fuel ratio.

Check for new codes then post them on here.

 

Ok, I finally pulled the codes, the only code is P0420.
I bought a non fouler for the o2 sensor so hopefully That'll solve the CEL.

Could clogged egr passages be the source of the problem?
What are the usual symptoms of clogging egr ports?

I don't really know if they're clogged or not, but the first time I seafoamed it, it yielded a huge improvement in low rpm.
That tells me this motor has seen some carbon buildup.

 

The seafoam probably won't clean out the EGR passages. You will have to remove the upper part of the intake manifold. You may also want to clean the throttle plate (both sides) and the bore of the throttle body.

What kind of NGK plugs did you put into the car?

 

The plugs I'm pretty sure are Iridium IX. They were like 7 bucks apiece at Advance.

If the computer isn't throwing code P0401, does that mean that it's not clogged? Is it still worth taking things apart to clean it?
Removing the upper intake manifold will be a first for me.


EDIT:http://www.youtube.com/watch?v=d8N-S...feature=fvwrel
This video answered most of my questions.
I'll give it a go, hopefully I don't screw anything up.
Is the silicon grease for the injector o-rings 100% necessary?

 

You want a good lube on the injector o-rings....a leak there is a BAD thing.