Employee can seek relief under Industrial Employment Standing Orders Act, SE act applicable to the state, Payment of Wages Act, ID act as per explanation of employee under these enactments or thru civil court.
Ideally speaking dues to the employee should be paid on last day in office or within 2 days. Majority of the companies cite internal policies of say 30 days, 45 days. You may refer to the standing orders of the company, employee rule book, HR policy handbook etc. All such policies should be kept within the reach and knowledge of the employee. Any policy which is not circulated and supplied can be questioned. If these policies are not available with you may demand these and also try and obtain from some colleague.
Instead of making verbal communications you may address written representation under acknowledgment to your HR contact and narrate all representations by phone ( mention phone numbers, date, time etc) and minutes of discussion, followed by escalation to good offices of your appointing authority, MD, Chairman, Company Secretary, with a copy to Head-HR and raise your queries.
As per notice period applicable to you notice pay can be adjusted in your FNF statement/settlement.
You may elaborate “shrinkage in stock”. Does it imply reduction in sales/market share/revenue etc or it pertains to some stock option extended to employee?
The policies, T&C, which are communicated to you and are not accepted by you do not form part of your contract hence it shall be difficult to apply these to you.
You may mention in gentle tone that the same is not applicable to you and company may supply you the grounds and evidence on the basis of which HR contact has stated on dated………that the same has been applied by company to you.
From your designation mentioned by you it is felt that you may be able to invoke the provisions of ID act. However you may let a competent and experienced service lawyer/Labor Consultant evaluate the merits.