If your D16W9 is in a decent working condition, don't swap it, unless you are getting the correct ECU and wiring harness for the new engine too. In any case, it's one of the best D series engines because of it's dual vtec.
I just had a bad experience with my 2003. It has a D17A2 now (single stage Vtec-e). It visibly loses power above 5500 RPM, because the D17A2 has a different, single stage cam. The car is ruined.