I would suggest the following:
1) Perception roll at -20 to be woken up from normal sleep. Modified by the sounds and/or actions of others (i.e. being slapped = +75, etc).
2) First round awake, make a Medium Self Discipline roll. Success = -25 to initiative for that first round; failure by 25 or less, -50 to first round's initiative; failure by 25-50, no action first round and -25 to initiative second round; Failure by more than 50, no action first 2 rounds, -25 to the third round's initiative. Modifiers due to circumstances can be applied here.
3) actions during the affected rounds receive a -25 modifier or take 25% longer to accomplish.
4) may make a new Medium SD roll each round, with success meaning you are awake, and failure means you continue as directed by the first roll (#2 above). Trying to "clear your head" and wake up is a 25% activity action.