I think 90 days you are talking might be 90 working days, so you might have applied before the deadline. About TPS extension re-registration, you can apply without EAD first, and once TPS is approved, you can apply for TPS EAD. I assume that you went to Nepal based on F2 status since TPS was pending during that time. Yiou just have to spend $ 85.00 for biometric. Good Luck.