How do I account for the time it takes for my engine to throttle up in my suicide burn program?

If you're still interested in making the program tho, take a reference of this craft.

Basic Idea is starting the suicide burn at DistanceTravel, adjusting your throttle by comparing AGL and DistanceLeft, and turning off your engine at DistanceTerminal. I tested it with the electric engine(almost instant throttle) and gas generator engine(2 seconds thtottle) and they all worked fine.

It might crash or not land for the slight error, smaller than few meters. it's because in SR2 height is measured from your craft's CoM and CoM changes as you burn the fuel.

I have the exact program dealing with this. Believe me, this is harder than you think. this is a part of the formulas I made to make the program work.

However, when it comes to your problem:
set Throttle to 0
set "throttleTime0" to timeSinceLaunch
set Throttle to 1
wait until engine thrust = max engine thrust
set "throttleTime1" to timeSinceLaunch
set "throttleTime" to "ThrottleTime1 - ThrottleTime0"

But if your wondering the fastest engine cycle to throttle up in the electric cycle

I used to worry about that, but I realised air drag and mass reduction due to consuming fuel will do more than compensation for the delayed full throttle. So unless you're using really big engines and in vacuum environment. Don't worry about it. Otherwise, set slow motion and put full thrust while the engine panel is open, see how long it takes and divide by the slow motion rate then maybe divide by 2 (if it takes 2 seconds to reach full throttle, I'd count 1 second only since it wasn't dead during those 2 seconds)