Hi and welcome to PedrosBoard.
Lets start with the functions of the CLU:
1.- It controls the windows
2.- It controls the convertible top
3.- It controls the Alarm
4.- It controls the Keyless Entry System
5.- It controls the Immobilizer function.
From what you've described, the CLU seems to be operational.
The two beeps when you lock the car means that there's an open circuit in one of the locks. (Doors, hood, trunk and/or oddment compartment lid and/or glove compartment if you have one).
It either fails or it works. It generally is not intermittent, meaning that sometimes it allows the engine to start and not others.
It sounds to me that you have a bad ignition switch whether it was replaced or not (you don't mention when it was replaced).
You could have a faulty cam position sensor as well.
When you say that the car doesn't start, is it the the starter doesn't crank or that it cranks but the engine doesn't catch?
Happy Boxstering,
Pedro
Pedro Bonilla1998 Boxster 986 - 311,000+ miles:
[www.PedrosGarage.com]
PCA National Club Racing Scrutineer - PCA National HPDE Instructor - PCA Technical Committee (Boxster/Cayman)
Racecar spelled backwards is Racecar
"Racing is life. Anything before or after is just waiting" ... Steve McQueen as Michael Delaney in "LeMans"
"If you wait, all that happens is that you get older"... Mario Andretti
"Being second is to be the first of the ones who lose" ... Ayrton Senna