I am also not sure whether you had to restore your status. When did you start counting for the 90-day mark? The day you got your final results or the day you got a graduation letter from your college/university?
But I don't think it would be wise to apply now, especially if your application is close to being approved. I have seen cases on the forum (this thread) where people have been approved for PGWP even if they didn't apply to restore their status.
When did you apply for the PGWP?
Not to add to your pain, but if they reject your PGWP and if it has been over 180 days since you graduated, you may not be able to re-apply for PGWP.