Weird idle then fine with cold start
 

First things first, I have an 04 6 port MT with a fresh rebuild. Car runs and starts fine (especially for a fresh rebuild). My issue is that it will start fine and then the idle will start to fall like usual. once it gets to about 1200rpm, it will "chug" for about 5 secs then return to normal. I have no power issues other than what I can only describe as choking if I hit the gas hard at idle. I am throwing a cel, but it is the p0420 and p0410 due to my cat being gutted and the air pump delete. Other than that, the car runs great. I did just notice today that my coolant fans stopped working as well, but I haven't had a chance to look at them yet, so I am not asking about that. Here is what I have done so far:

550 miles on rebuild
coils, wires, plugs
replaced coolant temp sensor
replaced injectors and fuel rails
cleaned MAF
cleaned SSV
replcaed ESS
replaced upstream O2 sensor, but not downstream yet
Compression is good, but still breaking in so a little on the lower side still

Using torque and MAF reading 7 when it happens (at start-up), but drops to 6 once warm and operating idle is around 5 give or take. 15-20% load on engine at idle. it doesn't change if the clutch is in, so I am pretty confident that it is not the neutral safety switch. Haven't done the thermostat yet, but from searching, it looks like I should. Really just looking for any ideas and things I might be missing. I am thinking it might be the rear O2 sensor even though the cat is gutted. MAF is getting good readings, but I have not ruled out the ECU.

Looks like you have done all the right things.. But, if it were me...

When it is cold, disconnect the battery for 5 minutes, hook it back up, with foot off the gas, start it and let it run until the fans come on, then drive easy.

Repeat again the next morning. There is some learning that has to happen. The MAF values look about right. Give ECU a chance to learn the motor. The process above does that.

It usually gets better for a few miles when I reset the battery. Only reset it a couple times though while I was replacing things though. I will give that a go for a few days and see how it goes. I usually only drive it to work and home but I will make a store run every few days. It was choking out while driving before I did everything, so it has gotten better, just not quite there yet. Thanks for the advice!

After driving for a couple of weeks and 2 ecu resets, the 8 is back to normal. Thx for the suggestion 04Green!