Ill give you my experience with what seems the same symtoms. I accidently misshifted from second into 1st instead of 3rd at about 6800rpm. Well you can imagine how that felt, but anyway, the check engine light was on and the car was running very rough, couldnt get over 30mph. Well I limped it home and the next day I started it and it was running fine. I drove it for a while with the engine light on and eventually it was running rough again, I would let it cool down, restart it and it would seem fine. After a few days of this I finally brought it to the shop. They said they would have to pull the engine apart to find out why, so $2000 later they found bent valves (not rods) but I would assume it would have the same effect if it was the rods. They told me that the computer would compensate for the compression loss and runn either lean or rich deppending on what it needed to stay running, well after so long of that the computer couldnt handle that and would actually shut those leaking cylinders down and that when the rough running would start. I had the valves replaced and the I ended up paying over $3000 for the job. If you are paying out of your pocket I woul dhave them replace the rods rather then the engine, I mean unless the block itself is damaged why would you need a whole new engine? That would only be easier for the shop. If its under warranty, well then I would definately go for the new engine. Let me know what happens, I would like to know for future ref. Thanks
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