In view of the above submissions my suggestion will be that
1. You should submitted resignation in writing to your superior and he/ she refuses the send the same through Registered AD post.
2. Request them for handing over charge you were holding.
3. Make a list of works you were carrying and status till date of your leaving.
4. Make a request to curtail or remove notice period.
5. Make your self available during working hours for their support within specific time frame.
6. Sit across table to resolve issue(s) amicably.
I do agree that you have not received any appoint letter / contract letter but keep in mind that you received regular salary during your tenure. Legally some of the terms are implied.
Hope this will resolve the issue.
First of all,there should be a written resignation and a brief of all outstanding points/advances etc.
If all sources of inflow into your bank a/c are identifiable as legitimate transactions their claims of you stealing funds will flop miserably.
Incentive due to you can easily be worked out so question of misusing trust and transferring money does not arise(if all what you say is correct)
Fact of drawing salary monthly basis indicates employment for legal purposes + your daily attendance records in the company.
Non deposit of PF money is a serious offence and if you complain with proof,then directors will be in big trouble.
Points of learned member above are valid and worth acting upon.
The matter is more than 4 years old why now things are being agitated /