In regards to the breaching pods, tweak their arrival and departure cues as you see fit. If they arrive too early, increase the delay of their appearance after the main fleet from 61 seconds to something higher. Then you simply need to edit their departure cue such that their departure location target is Babylon 5, and they head for it as soon as they arrive. The example below has the Breaching Pods entering the mission about a minute and a half after the main alien force arrives. A second later they head for Babylon 5's docking bay.
The mission breaking problem of hostile wings not registering as being destroyed can be solved similarly. I've noticed each of the hostile fighter wings has 2 or 3 waves of about 6 fighters each. They're set to launch from the enemy capital ships. What's probably happening is that the caps are getting nuked before every wave can be launched, and the mission requires
100% destruction of the enemy waves. When the arrival anchors for those fighter wings is removed from the mission, in this case the capital ships being destroyed, those wings stop showing up. Any remaining waves will not make an appearance, and when the game checks to see if a wing has been destroyed it checks to make sure all the
waves of that particular wing were destroyed too. If you blow up the first wave of a 3 wave wing, for instance, you've only done 33% of the work the mission actually demands from you. If the capital ship that deploys those wings gets blown up thereafter, before the remaining 66% can show up in the mission, this goal will never return true.
There are number of ways around this. For one, you can set the arrival location for all hostile ships to "Hyperspace" to guarantee all the fighters will eventually show up. Alternatively, do an overhaul of the mission objectives such that only partial destruction of the total enemy force doesn't break the mission.
