The system has about 4 seconds dela

The system has about 4 seconds delay. You can observe it from the impulse response or the measurement signals directly. You can try different initial guesses for the delay. The VI might not be able to find the optimal delay if you set the initial guess for the delay far away from the true value. For example, the estimated delay is zero when you set the initial guess to 1. If the delay is not correctly estimated, the error will be large in the transition points. You can see sparks at 0, 400, 800, 1000 and 1200 seconds in the Error (Measured - Simulated) graph if you set Delay Initial Guess as 1.