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Could the timing chain have jumped a tooth causing this low speed roughness? I am puzzled, any other ideas?
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These engines have steel timing gears with no nylon teeth. I have never seen a chain jump on one of these.
Being we are not sure what direction to look, here are a few things you should check:
Check the ECM for trouble codes. Let me know if you need instructions on checking for codes without a scan tool.
You could try disconnecting and plugging the hose to the EGR valve and taking it for a test drive.
Testing the coolant temp sensor is easy. Do a search with ChevyTech and coolant sensor and you should find specs and instructions.
If you have found no problem the next thing to check is fuel pressure and can post information on this if you want it.