Okay. I gave it a try and I spotted several things. Just looking at the mission in FRED now
1. You appear to be mis-using variables.
eg. in the first event you have this
There is no need to use a variable in this place. What you want is a constant. Most SEXPs that use numbers default to constants (usually 0) simply click on the number and change it to whatever you want (much like renaming a file in windows explorer).
Since you've now set this number to be a variable you may not be able to simply click and edit the number. You can simply change the expression to is-destroyed-delay or some other SEXP and just change it back again to return the constant.
Variables are used in more advanced situations. Unlike constants you can change the value of a variable the number shown in the brackets is the default value but by the time the Event actually occurs the variable could very easily have a different value.
2. In the second event you're using the set-unscanned SEXP to set the transports as unscanned. This is unnecessary as you can simply go to the Ships Editor>Misc and untick the cargo known box to have the same effect.
3. The Iota Chatter Events could be replaced by a simple Send-message-list SEXP. Chaining the events like you have done would only be useful in combat where there was a risk one of the ships might be destroyed (in which case you'd check for that).
4. You've beam protected Alpha and made him stealthy but the enemy will still take potshots at him from time to time. The solution to this is to have an event at the start of the mission which protects alpha1. That will stop anyone fro shooting at alpha.
Okay those are the minor things. Now for the big ones.
5. The argos have a habit of pushing the Iceni around. I've got no idea why they're doing this. Nor why they have a habit of pirouetting around like ballet dancers when they reach a way point. I'll take a look at the mission again and see if I can spot the cause.
6. There's not much for alpha to do except sit there. To make the mission more interesting you'll need to borrow an idea from the FS1 mission Playing Judas. Have the NTF fighters periodically inspect the troop transporters. Have them spend the rest of their time flying a guard patrol.
Then add an event something like this
-< (the less than operator)
When this event comes true unprotect and unstealthy alpha, send a message that shows he's been spotted (either from command or the NTF). If this occurs say that the mission has failed.
Add another (repeating) event with a 20 second delay or so that comes true whenever the player gets within 2000m of iota wing warning the player that he's getting too close.
Another way of making the mission more interesting involves the use of variables. Create a variable called eavesdroppingScore or something similar (one word, variables with spaces in don't work). Instead of playing every message only play them when the player is within 3000m of the Iceni. Every time a message does get played add one to the variable
modify-variable (The one in the replaceOperator>change>special menu not the first one you'll see)
At the end of the mission if the player has scored high enough he passes. If he was too scared of the fighters to get close to the Iceni he fails.
on the dialogue
Some of it will have to change as this isn't DEM II but it did make me laugh