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pull the plugs and see if there fouled out. we just put a rebuilt 4.9 in a ford over the weekend and it ran fine. then it started shacking real bad. it would idle good for a few seconds then start shacking real bad. had no power whats so ever. we took the truck down to the shop that sells the rebuilt motors and they agreed to look at it. turns out it was a bad pushrod or valve or something. might have even been a bad head gasket cant recall. hopefully in your case its not that serious and the motor just needs a tune up. good luck.
That happened to me as well. It turned out one of the plugs ceramic insulators was cracked and arcing to the block and another plug wire was arcing to the dipstick tube. I replaced all the plugs and wires and now it runs great.