Short version: To finally find resolution, I replaced both Cats with Magnaflow units and both O2 sensors with the
Amazon-Denso units. While the unit was up on the rack I went ahead and had the shop cut out the rusty muffler / resonator and replace it with a mild Magnaflow stainless muffler. With the new muffler I significantly reduced heat in the second row floorboard, gained a little sound, cut ~50 lbs from the system, and improved clearance at the rear with the new tail pipe ending just above the bottom of my ARB pig. . The original exhaust routing exited below the rear bumper for a little while. After a few steep descents, the tail pipe was naturally relocated with a new profile... The end result: The vehicle runs better than it ever has in the 2 years that I have owned it. I gained 2-3 mpg on the highway - city unchanged, acceleration is greatly improved, and the engine "just runs better" with the less restrictive system.
Part numbers used in the end:
Qty 2 O2 Sensors - Denso 234-4260 - $130.00
Exhaust system revamp - $770.00 out the door
Qty 2 Catalytic Converts - Magnaflow 99354HM
Qty 1 Muffler - Magnaflow 13235
2 new mid-pipe sections, same Y-pipe, new pipe / routing configuration from muffler to exit
Long story on how I got into the mess:
I apologize in advance if I repeat anything in this thread as I have not read every post, but feel certain that I have lived the same nightmare as the OP.
This past Thanksgiving night I lost my alternator on Interstate 85 just outside of Charlotte, NC. I have 190K on the 2006. Failure was immediate - heard bearing whine while at highway speed, lost voltage on gauge, and shortly thereafter the battery was depleted. I have an Optima Blue Top as a secondary and introduced it to the system with the 200A continuous duty solenoid used in the isolation circuit. This allowed me a few more miles but ended up on the side of the road with 0 power. I knew better than to push it but I was so close to the next exit I took the chance but lost in the end. AAA took care of me and had a local company pick up the cruiser that night, store it on their lot, and deliver it to my home in Greenville, SC the next morning.
I replaced the alternator with a Denso reman unit sourced from a local parts house and I was off....so I thought. I heard a rattle in the right Cat and had both 20 & 30 codes with MIL. I went through the same clearing, monitoring, testing....with TS and saw similar results as the OP. I looked for vacuum leaks, replaced the PCV, checked plugs, and cleaned the O2 sensors (in the Cat - left the AFR units alone) with no change in results. With the new rattle in the right Cat i can only assume I dumped some fuel into the Cats when I lost ignition, caused detonation, and "blew" apart the Cat.
I talked to a few performance shops in the area about alternatives to spending $$$$ for OEM Cats and while most said that Toyota's are a real pain when dealing with aftermarket Cats - apparently the OEM units are built better than most, are extremely efficient, and as a result, the ECU programming is tight and allows very little tolerance.
I found a shop that offered to replace both Cats with Magnaflow units and guarantee no MIL with proper system operation with a 100% refund with removal of the aftermarket parts allowing the OEM install. I figured I had nothing to lose and gave it a shot.
After cutting out the OEM units, the right Cat was in fact destroyed. No light passed through the unit and after punching the screen out of the exit, several pieces dumped out. The left unit, while not physically damaged, would not pass light and looked obstructed as compared to the new, higher flowing units.
I went ahead and replaced the muffler / resonator with a single Magnaflow muffler along with the Cats. I also replaced both O2 sensors at the same time. The sound of the new system is mild, but sounds like a V8 at startup / acceleration without a drone at highway speeds. Overall I am very pleased with the new system. The cruiser runs better than it has in the 2 years I have owned it with 2-3 mpg better highway economy, better, smoother acceleration, and the butt dyno says I freed up a few HP with the higher flowing system.
I have put ~1500 miles on the system in the last month with no MIL / Pending codes and and overall better driving experience. While I am a firm believer in using OEM parts, the cost of OEM in this case was several thousand dollars and just did not make sense in my opinion. Time will tell if the system performs as expected and keeps the ECU happy. I hope so but even if I have to replace the Cats 3 more times I am still shy of the total cost of the OEM job... A gamble I am willing to take.
Good luck with your journey and hopefully you will remain in the clear with the sensor replacement. If not, keep in mind aftermarket catalytic converters as an option to restore the efficiency the ECU is looking for. Let me know if you want to see any current TS data or have any questions around my experience.
-David