I am on the final mission of Mcaulife. I've beaten all the kilrathi fighters and auto piloted to the Tiger's claw, but then the transport starts flying in the other direction, and if I get close to the carrier to land, it says "Wait for Drayman" What should I do?

Do what it says! Make sure you're flying alongside the Drayman. Usually what it means when that message comes up is it is jumping into another system.

Actually it seem like the drayman is flying all the way back to the point where it jumped in on the other side of the map.

It's supposed to be flying to the Tiger Claw. Also I did follow it and it seemed like it would keep going till I ran out of fuel.

Actually, I beat the stupid level. I just didn't wait for the drayman, but instead landed immediately.

Is that how you do it? It keeps telling me the drayman was destroyed when I had my eye on the damned thing until it flew out. This has happened four times and it's driving me insane, especially given how long this damn mission takes.

Same thing happened to me, and caused me to ragequit the game for a couple weeks.
First, I didn't realize until I was almost done with Secret Missions 2 that there was an autopilot function, so in that mission I escorted the ship the whole distance manually. The first 3 times I just landed and was informed that the Drayman didn't make it. The 4th time, I followed the Drayman and eventually the Tiger's Claw spontaneously exploded. A few weeks later and the 5th time, I somehow made it. I think the trick is to follow the Drayman from behind, then once it reaches the Tiger's Claw and changes direction, very quickly land. I think if you let it get too far before you land the game will assume that you abandoned the ship and destroy it or something.

So no autopilot, and instaland as soon as it makes the turn?

I think it should be safe to use autopilot, just wait for it to start moving into formation with the rest of the fleet once you're near the Tiger's Claw, then land quickly.
Edit: Just finished it again with autopilot, and the Drayman did make it again.

You rock holmes! Tonight I will finally finish the Dakota system!

I know theres whole branches of areas that can only be accessed if you screw up the missions, but I'm not quite sure HOW I'm supposed to fail without super failing.

This game wrapping my head up.

Edit: THANK YOU! I was so close to just dropping the whole thing. Now to survive the infamous other hard mission...

There's a FAQ about the different tracks through the game, how many points you need to get to each series, etc:
http://www.gamefaqs.com/pc/938383-wing-commander-the-secret-missions/faqs/9829
You can also replay the missions you missed via a transfer program in Secret Missions, just make sure to backup your save file first as it will overwrite your data.