1999 LS1 M6 91k miles

After having new fuel filter installed and putting my NX Wet 150 back on (by pulling the shrad valve too), the car has a mis or stumble?

I have not run the juice yet since I am afraid I might cause damage.

I use to be able to start in 2nd from a dead stop, but this is when it happens.

It also happens if I am in a lower gear than I am supposed to be in...it will bog like normal, but than the mis/stumble will appear along with the bog?

It also was knocking/det from high 4's to 6k rpms, so I reset the pcm, and it went away for a day....now it is back along with the stumble again.

***I am getting P0430, 2nd bank, or, BAD CAT...comes and goes, but this has happened for years now...I just keep clearing the code. Could this cause this mis/stumble?

Could it be the fuel filter?
Could it be the shrad valve being taken out?
Could it be the spark plugs or wires?

Any ideas?

This prob could take a lot of trial and error until I find it.