J30 Idle/Timing, Emissions, ECU questions

[JDM Sam]

First Question:1993 J30 150k miles. Recent related engine work done: New O2 sensors, new head gaskets, new coolant temp sensor, timing belt/tensioner, plugs, new injector orings, egr bypass, coolant line bypass on intake manifold, K&N cone filter

Idles stumbles like a misfire. Not irratic, about 50 rpm difference.This local guy that knows about the the VG30DE says my timing is off, since the compression was good. Heads were torqued to spec according to Chilton manual so can't be the gaskets that were just replaced.I lined up the timing marks on the crank and cam pulleys when I installed the timing belt. The 300zx guy told me I still need to reset the timing via the CAS. How do I reset it on this car?What's the normal idle RPM for this car?

Second Question:I also plan on replacing the cats as they seem to have failed when 1 injector O ring wasn't seated right and fuel dumped into the engine. I hear rattling noises in the catalyst which is obviously they insides cracked. This should be the cause for the high CO content correct?

Third question:I removed the EGR system because it failed and bypassed it all together. I ended up taking the heads off the engine to unlock the motor from huge carbon sludge buildup (you scoop up a ton of it) which was piled in the combustion chamber somehow and caked in the intake manifold. I traced it to a failed EGR valve and the EGR lines were clogged. It was the reason it had starting problems from the get go. Hot tanked the heads and degreased the intake manifolds in solvent. Also bypassed the intake manifold coolant lines to the throttle body.

Do you all recommend to get the ECU reprogrammed or wire an S-AFC to control the fuel because I heard it bypassing the EGR causes it to run richer.

[jtesensky]

I hear rattling noises in the catalyst which is obviously they insides cracked.

Could be a rock...

Idles stumbles like a misfire. Not irratic, about 50 rpm difference.

Check your intake air temp sensor, was it removed or shifted with the add of the K&N? I have seen this happen to the P10 & P11 ricers.