Your answer to Question 1) So long as you have paid stamp duty on guidance value even if the value shown in the sale deed is much lower, it is absolutely correct and legal. I see no problem.
Q-2) You state that you registered the property at Rs.55.47 lakhs, TDS @ 1% must be deducted by you into the builders PAN No. online and paid by you. TDS to be reckoned on the total sale consideration value shown in the document.