Not 100% sure it is, but it sounds very throaty and no where near as smooth as it was a lil while ago, although it still drives....
my cars the V6, the spark plugs seem fine..... not really a engine man so im not sure where to go next... the garage maybe?

How much mileage has it got and when was it last serviced? Could need an oil change?...

well thats half the problem, it was only just fitted. replacement used engine.

it still drives fine, but will i damage the engine if i drive it?

So you've had a replacement engine fitted? Did you not get any history of the engine they put in? Not sure what it could be mate, If your really worried about it you may want to get it down a garage for them to have a look at, but as you say, it drives fine so might not be anything..

Sorry im not any more help...

are u using the spark plugs leads that came with the motor? You could try replacig them and see how you go. When i changed my motor over it was going ruff till i changed the leads and its fine now.