I have a 1998 5.4 liter expedition. I took it to the local Ford dealer, to have a problem diagnosed....it was missing. They told me it was a bad coil pack and an intake manifold gasket. They wanted too much money so I figured I could do it myself. I replaced the coil pack, and also replaced the intake manifold gasket...I followed the proper procedures to change the intake manifold gasket, all the nuts, bolts, and washers were accounted for, so I fired up the engine and I heard a horrible knock. The first thought was something fell into the cylinder..a nut or bolt, I located where the noise was coming from after taking the spark plugs out. I stuck a magnet down in there and got very small pieces of metal....after several hours of trying to get everything in the cylinder out of there....I got half of the bolt out followed by the other half a half hour away. It was one of the coil pack bolts, six months prior to this, I had a rear coil pack replaced from mechanic...and he must have dropped one of the bolts down, and it just sat there by the spark plug and he replaced the old one. So after dissembling the whole thing, and reassembling it again...I now have what sounds like a permanent knock that speeds up with acceleration.

My question is: Do you think that the skinny bolt I found bent my lifter..or could have done something else??
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It's probably a bent valve.

 

Could be a bent valve and that would mean that you still have a miss as the valve would not be sealing on the compression stroke, also might notice a back fire through the intake if it's an intake valve not sealing. Good chance you could also have piston, wrist pin and or rod damage, so now this just got real expensive.


Edit: Also want to add a cracked head is very possible.