knock sensors the problem?

I had knock sensors replaced along with the harness due to error code p325.
I also had the spark plugs replace along with the spark plug wires.
Here is what's happening. The engine ran like a top before any of the work was done but
the engine kept showing code...so I had all of the work stated above done. Now the engine misfires and runs as if it's dropped 2 of the 6 cylinders-but only for a little while. It clears up and runs fine (not as before the work, but ok). It then repeats....now it's been three separate episodes of doing this. No error codes yet-but cel blinked 3 times but did not stay on. I took the truck to a Toyota dealership and had them do diagnostics on it- they found engine knock was recorded but couldn't replicate. The sensors used to replaced the bad one/ones were not OEM.
Could the sensors be mistakenly thinking they sense knock when there is none and computer retards the timing when there really isn't a need for it to be retarded and this is what is causing the misfiring?

 

Take it back to the shop that did the work. They screwed something up. Reputable shop?

 

Check the motor and trans mounts, electrical grounds and wires for any burned or pinched wiring (especially around the egr valve)