Dear Alec,
To minimize the start-up transients, we always recommend that–at a minimum–the initial blade-pitch angles and rotor speed be set appropriotely for the given wind speed. It is also possible to set initial blade and tower deflections, but these are less critical. Regardless, even when setting proper initial conditions, it is common for the start-up transient to last for about 30 s, so, we also recommend that the first 30 s of simulation not be used in post processing. When simulating with floating platforms, it is also important to set the initial platform displacements appropriately for the given wind speed (basing the initial platform displacements on wave condition is less important).
To obtain the appropriate initial conditions, it is best to develop the relationships for the steady state values of each parameter as a function of wind speed, as discussed in the following forum post: steady-state responses of 5mw ref..
We are working on a new framework for FAST that will allow for the calculation of static equilibrium or steady state conditions at the beginning of a simulation, but it will be a while before this feature is available. I suspect this feature is too difficult to add yourself to make it worth your while.
Best regards,