Hi Seahawk-
I'm by no means an expert, but I have played several games of Halo, so I'll take a crack at answering your questions.
1. If this is a FRIENDLY boarding action, I'm not sure. I haven't ever encountered that issue (and I don't have the rulebook sitting in front of me). You might consider posing that question in the Spartan forums, but when you do make sure you explain (if I'm understanding you correctly) that you're talking about sending boarding craft to a friendly element to assist in defense against an aggressive boarding assault. I think they have an FAQ thread on their forum, you might want to peruse that because this question may have come up already.
In an AGGRESSIVE boarding action, after the boarding fight has been resolved and if the aggressor still has boarding craft on the enemy ship, you can elect to extract those boarding craft. However, if you do so, you have to be able to get to a friendly element that has room to take on the number of craft you're try to extract (so it has to be within 12"), and that friendly element cannot be under an enemy boarding assault. If you do try to extract, the enemy element you are leaving gets a point defense attack against you just like when you were inbound to board.
2. Covenant Defense Arrays (DAs) apply to all incoming fire, whether it is from enemy battlegroups or enemy wing formations. If the incoming fire is missiles (or if you're playing a Covenant-on-Covenant match, plasma torpedoes), then you would roll your DA and your Point Defense (PD) dice together in one combined roll (as opposed to other Spartan Games systems, where you would roll them separately). In the case of defending against enemy wings, you would fire your PD first, then the UNSC player would remove any wing tokens killed by the PD, then he would roll his attack dice against the element, then you would roll your DA. DAs will not help you against boarding craft; you can only use PD against incoming boarding craft. I do not know if DAs will help in a terrain collision, again it's a situation I've not yet encountered. I *think* that is covered in the rulebook. I know colliding with terrain in H:FB carries a pretty hefty penalty. Also, just looking at your list below, PD and DA will not help you once enemy boarding craft are on your ship--at that point, you are relegated to rolling your Security Detail dice.
3. Again I don't have the rulebook in front of me, but I do know the rules for this are laid out in the book. In some cases, an expelled boarding craft will not have to take a Heroic Save check; they can move up to 6" after being expelled the standard 4", if that 6" would allow them to land on a friendly element that can accept them (i.e. is able to carry boarding craft and has space to carry the number of boarding craft expelled). I believe this is why the rules usually say the craft is expelled 4" in a direction determined by the ATTACKER, not the DEFENDER, thereby helping the attacker to possibly recover the craft. However, in some cases they WILL have to take that Heroic Save. But again, I'm pretty sure this is laid out in the book.
I've loaned my rulebook out to a friend, so I'm just answering the above based on my experience and recollection. If I've given you bad information, then please accept my apologies.