2007 5.4 intermittenly runs rough then settels back down
 

Truck will start fine then after driving for about 10 minutes it will run really rough, the CEL will start blinking then just like that it will run fine again and the light goes out. I'm at a loss here

Your truck is misfiring
 

Search threads for diagnosing/fixing misfires.

Give us exact codes
 

Miles ,mods ,work done on truck ?Does it do it in higher gears ,climbing a hill after 45 mph . Last plug change ,type of plug .New boots /plugs mc /hosp clean job done correctly. This engine very fussy about proper plug job every 60k . Plugs must be torqued in 25 to 28 foot pounds ,done carefully and not by feel . Pull pcm and bracket to get to 3 and 4.
Frequent oil changes is key also .

Thank you for the reply,

153,000 miles
1,000 miles to next oil change
Plugs are 1 year old, not sure of brand was done by the dealer I purchased the truck from. if I had to guess they are not FoMoCo
Gear changes seem to set it off
Aftermarket exhaust is the only mod

No check engine light?

CEL will flash while it is running rough then it goes out when the motor settles back in..

Started doing it tonight going up hill...

A flashing CEL is telling you, you have a mis-fire condition. don’t trust that the dealer changed the plugs or at least used the proper plugs.. Replace all 8 spark plugs with SP546 plugs and a new set of boots and springs.

Ecobuilder , redfishtd , & techrep 'tells you no lies'.

I would also say that at that mileage you are entering the timing chain replacement territory. ESPECIALLY if you do not STOP the misfires and the HARD BUCKING that it causes. That makes chains slap those plastic guides to bits to go into pan an clog Oil Pump pickup screen - causing oil pump cavitation and serious oil pressure issues. Goes downhill fast.

Also, The PCM is doing its best (actually trying its best to take care of you). It actually cuts off fuel to the misfiring cylinders when the CEL starts flashing to pump fresh air to the CATS to keep from damaging them. That's what makes the CEL go back out, and then the PCM re-starts the injectors ---- so It settles back down. Smart little 'bugger', that PCM

Attack those misfires right away.