RX8 dies when clutch is pressed.
 

I have an 05 manual RX8. I recently replaced the engine due to busted seals. When I start the car, it seems to run fine. After driving it for a little bit, if I press the clutch in and let the RPMs drop, the car dies. It happens when I come to a stop and hold the clutch or put it in neutral. I can keep the car running, as long as I gas it enough to keep the RPMs from hitting 0.

Sometimes I will get a delay in response time of me pressing the gas, when coming from a stop. Other times, the car will act as if the engine has died (I get the dash lights and all) but, if I try to start the car, I get the grind when you start a started car and then it feels as if the car started back up again. Most of the time, it dies completely and I have to start it it over again.

At first it would take a while before it would take effect, but now it's after driving couple blocks.

On occasions the car will not die, but the car will sputter, and the RPMs will fluctuate between ~100 and ~2K RPM.

At first, there was no check engine light, but now I am getting the codes P0301 and P0031, which are Cylinder 1 Misfire and 02 Sensor problem.

I am in the process of replacing my catalytic converter, as I've read around and found similar, but not exactly the same problems I have, but it's due to a clogged/busted CC.

I was just wanting to get opinions from others to see what else I should look into as a possible cause, in case I am overlooking something or not looking in the right place.

I had the same symptoms the last time I had my engine replaced. It was due to low compression. Performing the SeaFoam/ZoomZoom Cleaner treatment on the engine might help. It can't hurt. Check the DIY section for instructions.

Bad idle can sometimes be an air leak somewhere past the air mass meter. Check all vaccuum lines, pvc, etc.

Sounds like a new O2 Sensor would not hurt either.

Hopefully you did new plugs, wire and coils when you replaced your engine.

Thanks for input, I will look into the seafoam/zoom zoom cleaning. See what I can find.

And yes, replaced plugs/wires/coils. I've already replaced the O2 sensor once, about a week after the change, and the new one marks bad after another week. I am replacing both sensors with the cat, just to make sure.

I had the air leak checked once, but I don't think it could hurt to go over it once more, but to follow up. The idle doesn't get bad, till after the car has been running a bit. After the car has been sitting for a few hours and I start it up, it runs great. It's just after riding a few blocks, and I come to a stop, I get bad idle. Assuming the car didn't shut off.

Make sure the nipples on the aluminum part of the intake manifold (on the passenger side of the engine) are either capped (which I think is the case on 04/05s) or connected to the PVC vent lines. A vacuum leak there will raise havoc with all kinds of stuff.

Same Issue
 

I have an 05 Manual, she ran beautifully before. Got flooded, had the dealer deflood her and now she has this issue. Did the cleaner work? I'd appreciate the input. Thank you.