Hello Rj Kadam,
I was going through your query and I understand your concern really well. Here is my advice:
I would like to tell you that the registration of the sale deed of any property is a necessity and can cause severe issues in the future. The same thing happened with you as the primary issue of your case is the lack of the registered sale deed document.
Since the lack of your document is causing a legal hurdle, you can still get the registration done by paying a penalty under Section 25 of the Registration Act of 1908. There will be some problems regarding this but upon request, you can still get the registration done.
As you have mentioned, the payment of the stamp duty has been done under the Maharashtra Amnesty Scheme (1994), You must understand that this is not enough. You can move to the office of the Sub-Registrar of your concerned area requesting the registration of the sale deed. There are chances that he will require the presence or statements of the builder, (in the absence of the builder), you can approach the court regarding the relief and seek an order for the registration of the sale deed.
While applying for the deemed conveyance, in the absence of the registered sale deed documents, you may also request the society to submit a declaration acknowledging your ownership along with relevant documents such as property tax receipts, MSEB bills, stamp duty payment receipts, etc.
Apart from all this, you must approach the registration of the sale to avoid any further issues regarding the property in the future and can get the work temporarily done with the help of the relevant documents like property tax receipts, utility bills, etc.
I hope that I was able to resolve your queries and still, if you have any follow-up questions, feel free to ask.