I have a 2003 Toyota Matrix XRS, 220k miles with the 6spd manual.  Car has been solid since I've owned it, all I've had to do is change the serpentine belt, plugs, 1x coil pack, 1x starter, and a couple batteries.  Oh, and the fuel tank is slow to fill...still not sure what that is about, but its just a very minor inconvenience at times.  

Couple days ago, it started having an intermittent miss/"stutter".  It was a somewhat sudden start, car had been driven around 140 miles and parked for a few days...next time I drove, made it about 6 miles when it started.  Now, its kept the P0420 code for several months (check engine light has been on), which I have always assumed was one of the two 02 sensors.  Before the other day, the car drove great, even with the code.  When the "miss" started, the check engine light flashed a few times, and stayed illuminated as before.  The misfire is at lower speeds in higher gears, keep it under load and it doesn't seem to be an issue.  In fact, at highway speeds, it never even shows up.

Today, I finally had a chance to run the codes.  I assumed it was likely another coil pack, but the code it threw was P0128...which seems to be a thermostat stuck open.  Odd thing is, I cleared both codes and it seemed to clear the misfire  I drove it a few miles, and wasn't able to get it to repeat.  I'm going to drive it again in the morning, and see if it does it again.  I have an AutoLink Al619, which will do live data, but not sure if it records misfires.

Any suggestions on what to check next?  Any way to test O2 sensors, or with 220k miles should I simply swap both out?  Thanks!

Replace the thermostat and check for vacuum leaks.

Check coolant temp sensor for chewed up wires first.

Might be time for a cat and or an O2 sensor.

I'll have to check the temp sensor, that is a good sugestion.

I went ahead and picked up a replacement 180* thermostat, but oddly enough, I recall seeing the operating temp of 180* last night on my code reader.  I also picked up an O2 sensor, I'll go ahead and swap the upper one.

I did get a little *miss* occasionally today while driving, but not as pronounced as before...and not quite as repeatable.  It hasn't thrown another code, so it has me a little stumped.  Coil packs usually throw a code, and all the plugs were replaced in the last 25-30k miles.  Not sure if its an injector, I'll have to figure out if any of my code readers will log live data/misfires.

Nvrmind

The Upper is an air/fuel sensor that measures if the air/fuel mixture was burned properly.

The lower(rear) O2 sensor looks to see if the cat is doing it's job properly, if it's not it'll throw that "cat below efficiency" code.

I think there are different codes for them, I don't remember.

I had an '04 Pontiac Vibe (same internals as Matrix) that threw a P0420 code after a little over 100k. I assumed it was the O2 sensor, but never noticed any driveability issues and didn't have to do an emissions test so I left it.

I've heard that generation of Toyota catalytic converter can go bad relatively early, so it may be yours has gone bad, and an O2 sensor swap isn't going to fix it.

Toyota TSB for P0420 states an ECM recalibration and replacement of front pipe (cat)

Is there a simple/easy way to test a catalytic converter?

I went out in the shop last night, planning to swap in a new thermostat and O2 sensor.  Well, the thermostat is completely buried under the intake, so I quickly gave up...had too many other projects to try and get done.  Plus, I was worried I would inevitably tear the t-stat housing gasket, and had no way to pick up/make another.  So,  put it on the lift, thinking I could at least swap out the upstream O2 sensor.  Nope, Toyota uses some sort of grommets for the wiring...no simple harness to unplug.  It actually makes sense, as they would likely be torn off from road debris due to the location.

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You just pull the grommet and the connector should come out just enough to disconnect it.

I figured as much, but didn't want to take a chance until I was sure.

I drove the car around 140 miles today, and did great.  I had a couple "misses" in high gears at low speeds, but nothing consistent (and very few occurrences).  The check engine light never did come back on, and I checked the ECT while driving with a scan tool and it was showing 172-174*...thermostat is rated for 180*.

Don't pull too hard, lol.

Might still have to go through the interior driver side footwell to disconnect the connector.

These look to be on the passenger side.  Do you really have to go in through the interior of the car to disconnect?