The system is not causal, that is why the use of identification techniques dedicated to the causal systems is risky and can't give good results. I propose a document to address this issue, witch the theme is 'Identification of fractional order systems using modulating functions method'. This method, we do not need any initial values which are usually unknown and not equal to zero.
Classical identification methods eg. linear regression LSE (System Identification: T. S. Soderstrom, Petre G. Stoica, et cetera) have good result for Gaussian noise on output and process variable. For noise on input obtain an acceptable errors eg. of quality index for the task LQ trajectory stabilization.
Regarding to the modulating functions I wonder what that function does do ?
Is this function a filter to estimated the expected values in the measurement points eg. for the ARMAX model?
or
Is the function a reconstructor of the transition of system from zero initial conditions to the current state ?