Hello, I'm hoping someone can help me out here or at least give me some ideas of where to begin!

Brief background -
My engine in my car was burning oil, smoking quite badly and rattling/pinking on light acceleration etc.. so I decided to source a lower mileage (64k) engine and replace it.
Whilst the engine was out I replaced; cam belt & tensioner (also other unrelated items).

Now the issue-
When I first drove the car after the engine swap it made the same bloody rattle but after lifting the bonnet I found one of the breathers on the inlet manifold split so I replaced all of them including the PCV valve this stopped the rattle ALMOST completely however it is still there but not as loud and not as often. Now I know this engine did not do this in its previous vehicle so there must be something on my car that's causing this....but that's where i'm stuck!

The rattle seems to happen on light acceleration between 1500 - 2200 rpm
Also it doesn't happen when the engine is cold

Another issue which may be related to this is that when i come to a stop at a junction for example the revs drop slightly and the car will shudder as if its going to stall.

HELP!