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At first I had many codes, I replaced wires, plugs, oxygen sensors (both) cleaned EGR tube from exhaust manifold (bad carbon buildup) serpentine belt and hoses. Flushed cooling system. (Engine 3 years old) changed oil. Reassembled and checked operation -
 I had 4, 5, and 6, cylinders wired from the ignition controller (coils) in same order. backfired plenty, checked order and re-wired right side of ignition controller (coils) to 5,6,4. Wired right ran great. Drove to work, and on way home check engine light came on. Ran diagnostics with Bosch OBD-II scanner -P-0304 Cylinder 4 misfire Checked #4 plug - looks good / fire good Reassemble- cancel codes.
Drove to work next day, on way home Check engine light flashing, (for a few miles then stays on,) then off then back flashing, then now staying on. Ran diagnostics - P-0304 Cylinder 4 misfire I pulled the EGR and it has carbon build up inside.
My Question is should I replace EGR valve? Should I disassemble engine further to clean pass the EGR?
Vehicle: 1998 F-150 V6 4.2L Automatic, 260K on Vehicle / 16K on engine (3 s old)

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If the EGR was to a cause a misfire condition it would set it on the number 5 cylinder , what you just may have is a faulty ignition coil, You disconnect the vacuum hose to the EGR if the misfire comes back , the coil would be suspected

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