Spuddering while accelerating.
 

I have a 2007 f150 v8 5.4 with 90,000 miles. I noticed that when I would accelerate from 40 to 50-60 it would spudder. So I took it back to the dealer and they put a new transmission in it. Got the truck back and it still did it. So they then put 8 spark plugs in and 3 coil packs. That fixed it but I noticed yesterday I was going about 50 mph and it felt like it was missing and then the check engine light blinked for about 10 seconds. Anyone have this issue

Flashing is indicative of a misfire condition.

Take it back to the dealer and tell them. They have specialized scan tools that can read this.

I hope you didn't pay for that transmission, because that's almost always a misfire. They should have replaced all the coils.

Oh no. I haven't paid for any of it. Almost everyone I've talked to has said its the coil packs.

Not trying to quibble with you - but you don't have coil packs - they are COP (coil on plug). Coil packs serve multiple cylinders with spark plug wires.