Delayed penalty not paying by the builder and charging interest

I booked a 3 room flat in July-2010 with a delivery timeline of 30 months. The builder has now issued me the offer of possession letter. There is a clear delay of 2.5 years from the promised delivery date. The contract has a penalty clause. The offer letter issued by builder states that the builder is not liable to pay any penalty if there was any delay in past in the payments made by customer for the demands the builder made. The builder has even added 40k Rs as delayed interest to be paid to the builder. This has come as a surprise as the builder never told me about any late payment and even no late reminders. I have always paid on time except one installment late for other charges due to service tax added. Builder also refused to take the principal installment amount if not paid service tax. It seems the builder is playing all kind of tricks to avoid paying any penalty and asking me to pay interest for getting possession however already paid 100% payment to builder except interest 40k Rs. I have discussed multiple times but builder is not ready to negotiate and not ready to pay the penalty. I have following queries: 1. Can builder deny me delayed penalty in case of any delayed payment by me? 2. If i pay delayed interest 40k. Am I liable to get penalties later post getting possession? 3. In case the negotiations doesn't work in my favor, shall I take the flat possession first and then file case in consumer court?