If the answer to the above is no, then you need to go and meet your former boss and take his help in resolving this matter as amicably as possible.
As told by Mr. Banerjee it is not a easy go for legal with the company, if your appointment letter states 90 days notice period/pay you have to fulfill the same. Your Boss who has approved the waiver of notice period/pay, is he authorized to waive off the notice period/pay please confirm. If he is not authorized your legal battle will be a mere waste of time and money.
Don't assume or come to the conclusion that legal is the only way to fight for your right.