Since the misfire shows up on the timing light the assumption is the misfire is due to a lack of spark. The ignition coil gets only one signal to fire spark from both towers from the ignition control module (this is because both towers belong to the same circuit inside the ignition coil). So, if only one tower is firing off spark... there'* something wrong inside the ignition coil itself. Since you are getting spark off one tower from each of two coils, but not the other tower, it would indicate the coils are bad. I know you changed coils, but just for *&G'* change the 5/6 coil pack over with one of the other positions and see if the misfire follows the coil pack.
Ignoring signs it seems to be a spark issue, another issue that could cause misfire on 1 and 3 is a bad intake manifold manifold gasket. Any loss of coolant lately?
Like Justin said, check the connector at the ICM.
2001 Bonneville SSEi (retired at 365,000 Kms.)
2014 Jeep Grand Cherokee Overland (yes, I know its not a GM)