Deduction of 68 days salary after leaving organization

I worked for an organization called "World Institute of Sustainable Energy" (WISE) in Pune during July 2012- Feb 2016.. The organization is registered as a trust under the societies registration act 1860 and Bombay Public trust act 1950. Since last one year (2014-15) the organization started facing financial issues and was not paying salaries to its employees properly. In my case, I left the organization on 26 Feb 2016, my salary was unpaid since Oct 2015-Feb 2016 (5 months) as the organisation was facing a financial crisis. One day after leaving the organization, on 29th Feb, I got a mail saying, 68 days leave will be deducted from my pay on the account of latecomings. The organization had arbitrary unwritten rules related to leaves and latecoming, such as 3 late comings = 1 day leave, Earned Leave starts after 11 days Casual Leave, and if a person takes even half day from office in EL, it would be considered as full day leave. Another arbitrary unwritten rule was if the employee took half day/full day leave prefixed and suffixed with holidays, the holidays were also counted in the leave. To illustrate: Suppose Friday and Monday are half day leaves, then the total leaves would be counted as 3 days (considering Sat and Sun as holidays). I called and mailed my office that I would like to be compensated for entire amount Rs 240058,but they insisted they would pay me Rs 119890 after deducting 68 days salary (in addition to deducting earned leaves of 90 days). Even this Rs 119890 was credited to my account after several mails and calls. Now they are saying that I was given a circular dated 1st Sept 2010 (when I wasnt even in the organization), whcih specified the late coming and leave deduction rules. Accordingly I would not be paid a single penny. Moreover, the organization have not even filed my income tax for FY 2015-16 yet. As the company is not ready to pay me remaining Rs 1,20,168. Please suggest me the right course of action. Note 1: I was not given any manual or written document related to leave or late coming rules in my joining letter or at any other time of joining the organization. Note 2: Even all my ELs have been deducted on this baseless basis, which being the good person that I'am ,I haven't claimed. Further, the organization has had a history of paying late salary to its employees on which I havent claimed any interest or penalty charges. Suggest whether I should now claim these charges as well