additional charges put by builder at the time of Possession.

1. I had booked a property in Jan2011 at Noida Extension, Uttar Pradesh (Financed through Bank loan) 2. My payment plan was Flexi Payment plan. 3. The property was supposed to be completed by May2012 as pet the original allotment letter 4. There was a dispute in the area with farmers and the construction in the whole region was stopped. 5. As per my payment plan, I was supposed to pay 40% with in 60 days of booking; but by that time, because of dispute, the banks refused to disbursed the loan(my loan was already sanctioned till this time). 6. In May,2013 the work was resumed and the demand letters were sent. At this time, I applied for a fresh bank load and made the entire payment as per the demand within the grace period provided by builder. 7. Now, in May 2015, builders have sent me the possession letter with the final 5% payment due on the flat and also the heavy penalty interest on the 40% payment that I didn't made within the 60days of booking. 8. In addition to above, they have also levied heavy escalation charges. My Queries 1. Should I accept the offer of possession? (I came to know that builder has only applied for the completion certificate but do not have it yet.) 2. If your advise is to accept the offer of possession, should I pay all kind of charges demanded in the letter (and mention unreasonable demands as "under protest" ) OR can I accept the possession by paying the valid charges only and for other charges mention it as "under dispute" and are on hold until final agreement arrives. Please advise.