1) First you take flat's possession in your hand and what he had forced you to signed that won't make any difference once society is registered and the building and its premises is handed over to society.
2) Actually this is not right time to fight with him because your amount has been invested and its chances to get spoil if you go against builder.
3) Wait for few days any how flat and construction is new, so you won't need any changes, but you can make interior and inside changes of flat, except already which are passed by municipal in layout that you won't changed it.
4) For today uses he is harassing like wet clothes should not hand in balcony for dry etc... So ask him to provide alternative option for all his restricted clause which mentioned in extra agreement.