If it's in the UK, you must tell DVLA the new engine number and send your V5 off for them to record the change. DON'T try to change the number by grinding it off and trying to put the old one on, as that makes your bike look like a 'ringer' and the Police may think that it's dodgy.
You can change the colour, engine cc, etc. easily - just fill in the relevant boxes on the V5 then send it off. You will also need to tell your insurance if you are fitting a bigger engine and you need to have the licence group to ride it (i.e. over the age of 17 with a CBT or a full licence).