the receipt from scrapyard does not mention engine cc does it ? it will be your choice to be honest or play trick.
you need to apply at excise mvr office islamabad with scrapyard receipt mentioning the engine number. fill out the form attach the receipt and original papers / file of the vehicle along with cnic copy. As precaution you can check the status of scrap yard engine number from islamabad police ; sometimes stolen vehicle engines are also sold at scrapyards.
if the engine cc is modified the annual tax / road tax also change. however you may get waiver for annual tax for car being over 15 year old.