Po136 Misfire, Or Other?

01 GT convertible w/ 70k miles.. Stock engine/auto with 70mm TB and CAI..

Check engine light came on a little while back right after I had to get the A/C line replaced under the CAI box. Came back with P0136 (right side rear o2) and P1000 codes. Car started running "rough" about 2 weeks ago - rough idle, bogging under throttle, almost as a misfire. Used my tuner to "turn off" rear 02 sensors, cleared the codes and resumed driving - issue came back again this morning - usually seems to occur after about 45min of driving..

So far, I've turned off the 02 sensors (no light on, yet still have the same "rough" running), reset the CAI box and cleaned/oiled the filter, changed the fuel filter about 3 months ago (when replacing the rear tank seal), checked and cleaned my MAF sensor, and throttle body - I ran injector cleaner through the last tank, and used higher quality fuel the last 3 tanks. No vacuum leaks, nothing left except 02 sensor, which is off, via the tuner .
If the 02 sensor is off, it couldn't still affect the performance, could it?
Could something else throw the code - intermittent coil pack? - not throwing any codes for that..

Help!
 
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