For the first event, you want to be using a trigger count instead of a repeat count. In really simple terms, repeat count says 'once this event's preconditions are met, repeat it X times, even if the conditions aren't met.' Trigger count says 'once this event's conditions are met, check whether the conditions are met again - and if so, repeat the event.'
To avoid the event triggering over and over again in a row, you need to set up a variable that indicates whether Alpha 1 is currently rearming. Add a variable called RearmingNow or something. Add another condition to your first event: RearmingNow = 0. Have that event set RearmingNow=1 after it does everything else. Give it a trigger count (say, 5) and a reasonable interval time (say, 30 seconds).
Then, have your second event set RearmingNow back to 0.
The last thing to deal with are your chains. I'm a little spooked by chained events involving trigger counts - I don't know if my superstition's up to date, but I don't think they work right. So what we're going to do is make your events work without chains.
Your first event is obviously fine on its own.
Your second event needs to say 'once that first event is true, plus a short period of time, I'm going to fire'. (How long do you want it to be?) How do we do this without a chain? Let's build a timer!
Create a new variable called RearmTimer. Create a brand new event. Give it a trigger count of 100 and an interval time of 1. Call it 'rearm timer' and tell it to say 'when RearmingNow = 1, modify the value of RearmTimer like this: (current value of RearmTimer + 1)' This variable will count up once a second when rearming is underway.
Go back to your second event, 'rearm complete alpha1'. Instead of true, set the condition to, say, RearmTimer = 10 (for a 10 second long rearm.) Then add a modify-variable to that event which resets RearmingNow (your first variable) to 0.
Now we 'rearmcomplete alpha1' should trigger 15 seconds after your first event triggers, no matter how many times your first event has triggered.
I'll leave the third event for you to solve using these tools.
There are more elegant ways to do some of this stuff, but I think this is a reasonable intro to variables. Anything you want me to explain in more depth?