Normally such things should be discussed before token. Not after giving token.
Since govt. took responsibility to issue the original number plates by themselves, the cost has become sky high. And hence majority prefer to arrange after market plates rather than paying huge amount to gvot. Which really doesn’t make any sense.
If the original number plates are lots by ex-owner, then its his responsibility to give you the copy of police complain about these plates. Otherwise same number plates will be running on some other car in some other part of the country.
If you are from Lahore, I can give you agent to discuss this matter. He can tell you the exact cost & time for issuing new plates through proper channel. You can also take his services for transfer of ownership too.
Having different engine number is common problem but not very serious. You can bring it to the notice of agent at the time of transfer and he will make the correction on the new smart card with current engine number.