For a proper advice, documents will have to be seen. 

If registration is mandatory as per the laws prevalent then, then you have no recourse but to file a civil suit for injunction against others from disturbing you as you have had possession for more than 20 years.  By all means you should keep possession of the property.  If society was formed after your ownership in that case also you can see the building plan or floor plan which must and should mention the number of shops. If not, you can complain to the Cooperative Housing Ministry. An Administrator may be appointed. 

Yes you can do so. 

Yes you can use amnesty

You need to take courts help as builder is not available. 

Filing a suit in civil court

You can avail of amnesty scheme and pay the stamp duty 

2)deed of confirmation can be executed by builder duly stamped and registered 

3) builder presence is necessary for registration purposes 

1.  Despite non-payment of Stamp Duty /Registration and not being a CHS member, the said property can be Gifted to Mother or you, by a duly Stamp Duty paid Registered Gift Deed, by annexing the Municipal Bills & other available documents.  AND thereafter you can sell /transfer /Gift /mortgage /whatever .... on basis of the registered Gift Deed.

2.  It is absolutely NOT necessary to become a member of the Society and nobody can force you for membership.

The scheme applies to all the transactions of sale or transfer of tenancy rights, of residential houses within Maharashtra. It even covers any instrument purporting to allot, transfer or sale any of the units in a housing society, which are eligible for deemed conveyance or for which deemed conveyance is pending. It also applies to transactions of allotment or transfer of all the immovable property units, whether residential or non-residential, of CIDCO, MHADA or SRA.

2) you can execute a gift deed if you have clear and marketable title to property 

Apply to registrar to issue summon to the executant of the deed and/or other witnesses to the deed requiring him to appear at the registration office either in person or through authorised agent in order to complete  the registration process.

Registrar has the power to take all necessary steps to complete the registration as to civil court.

You will be treated as a special case in the above matter. You need to approach court if the authority is not co-operating you. 

Under amnesty scheme, try to get it registered otherwise penalty will impose. Presence of builder may not require.

GIFT deed can be possible but title of your father is disputed due to non registration of sale deed. So get it correct first.

Once it is done, no need for gift deed.

But I understand that to take benefit ot Amesty scheme we need to be member of CHS? ---- NO

You need to file a suit for adverse possession against builder and society for getting ownership of that property because you cannot get ownership of commercial property on a stamp of 10 rs.

1.  The builder who sold the property ha to execute a registered sale deed in your father's name after which your father will acquire clear and marketable title to sell the property.

He cannot get the property registered by himself.

2. Yes, you can try this option.

3. No, you may not be permitted to transfer the same by gift deed to your mother without clear and marketable title to do so.

4. If builder is not traceable then you may have to approach court to get a direction to the registrar for getting the property registered.

you are right, a non member may not get this benefit.

Without a registered document on his name your father may not be able to transfer this property by a registered document to anyone including the proposed gift deed in your mother' favor

1. Now my dad want to sell the property. Can I pay stamp duty and do registration? Builder is not traceable now


Answer: Yes you will need to pay the stamp duty and registration as of today's date;

2. Can I go under Amesty Scheme recently launched and valid till 31.12
Answer: Yes you can be eligible under the amnesty scheme;


3. If registration is not possible as builder is not traceable then can we pay stamp duty and subsequetly gift that property to my mother or me and do registration of that Gift deed?
Answer: You will have to issue an advertisement in the newspaper;


4. Is there any other solution to clear my the title of property?
Answer: You can file a suit for declaration of the property in the civil court. Obtain a court decree stating your title and ownership of the property.