1. You can protest their decision to force you to accept the lopsided agreement and conditions.
If you have no alternative than to take possession, you can point out the incomplete work done by them and make of list of work that are to be completed and get an acknowledgment for that from the builder before taking possession or do not take possession, you may issue a legal notice venting out his grievance along with your demand for delay in handing over the possession or completion of construction and also you may demand the OC/CC before handing over possession of the flat.
2. They are to provide the OC or CC and also the builder has to make the flat ready on all aspects for the inhabitants, you have all rights to inspect before moving into the flat.
3. Decide based on the circumstances.
4. You can very well demand a copy of the agreement, it is your right. Let the builder deny you the supply of the copy of agreement and the conditions therein, you can issue legal notice or include in the notice this also as a demand from your side.
5. You can ask the reason for court fee, because where is the court involved in the registration. Please clarify that it may be registration charges, which can be paid by cash.