lot of questions let me straighten the list :
1- Yes after swapping it can become hell if it was a scrap yard gold hunted engine (learnt the hardway)
2- Engine number is updated by the verified custom clearance papers or a shop letter head reciept which has to be submitted along the registration file to the excise for a motor cycle the fees are 1200PKR these days to update engine
3 - If u do not have papers than its a stolen engine ? becuase even an NCP bike has a reciept when you buy from importers from taftan / quetta e.t.c... its a big market whole Gilgit agency uses NCP vehicles and huge quantity of cars are sent there with proper recipts under NCP flag and no registration.
4 - Carby / EFI what and which one ?