1999 Malibu - Intermittent missing

I am having a problem with my malibu. It is having an issue with intermittent missing. I feel it when I am sitting at stop signs idling. I don't notice it when in neutral or reverse, only in drive. Doesn't seem to be effecting the get up and go of the engine.
I am pulling 3 codes:
PO122 - Throttle Position sensor
PO401 - EGR system fault (exhaust gas recirculation)
PO420 - Catalyst efficiency low-bank 1 (---this one we have been getting since we got the car, change of catalytic converter and engine hasn't made a difference)

We did pull the Throttle Position sensor a couple of weeks ago to look at it; put it back on since we didn't have a replacement. For about a week it didn't seem to miss on me.
Does anyone think that this is what I need to change? Should I look at something else?
The car does start kind of hard when it has been sitting and the engine is cold, too; fires right up when warm, though.
I need some ideas if anyone has them!
Thanks!

1999 3.1L Malibu LS
Rebuilt engine 45,000 miles ago; new head gasket @ 36,000 was sucking antifreeze into oil.