Ok I have a 2005 LS HB with 190K on it. I am having rough engine issues. I have replaced the plugs, plug wires and coil pack. On the coil pack I did notice that cylinder 2 was rusty when I replaced it. So after replacing all this I still get the engine and hold light flashing and rough running. When I first start off in the morning there are no issues. I drive for 5 miles to get coffee and when I restart the car is when it happens. So I have found that if I turn off the car in neutral and restart the lights stop flashing and car runs fine for the rest of my drive into work.

For the drive home its fine until I get in bumper to bumper traffic (15 miles or so). Then runs rough, lights flashing. I just will continue to drive in traffic and after a few minutes it stops and all is good again.
Is there something electrical that I am missing? I am at a loss and don't want to really pay for someone else to work on it just yet.