Thought I would update this post for the moderators, as I believe it can be closed. It appears I was doing a few things wrong when setting up this mission.
1. As per Steph21 comments above, don't load the 530 missiles when you are carrying AG ordnance (Thanks for that tip).
2. Have a slight dive angle towards the target to get a successful release of the GBU.
3. If you intend on using a JTAC for lasing targets, minimize the amount of waypoints for the airborne drone (ie./ place unit down and give it a single WP over the target).
4. When using an airborne drone to lase, set the last WP to "Orbit", as it seems to maintain lock better on the targets below it. NOTE: If you have it in "Race Track mode", it tends to break lock in the turn and thus why the bombs were missing (no laser LOS/no target).
Hope this info helps someone else out, as I lost a lot of hair today