I'll answer your first question. Yes I will cover the top at some stage, As I mentioned it's a W.I.P or sneak preview and by no means finished.
At some stage during my builds I substitute bricks I dont have with a closest colour match to see what it looks like. In some cases I leave things as they are, with the colour differences on the container it could be used to similate wear and tear on the container or I could just go and replace all the new bricks with old pieces and vice versa.
I guess its more time vs money. The two colours are Light Bluish Grey and Light Grey, I prefer to use the light grey because its a more natural colour and more widely available.
The other issue is that sometimes sellers on bricklink have different listed greys than the official lego shop, in the floor tiles they are listed as light stone grey which i got from Lego's official pick a brick, there is no Light Stone Grey on bricklink.
I definately might go back and replace some of the parts at a later date, and as I mentioned above its by no means a complete finished project yet, I have quite way to go before its finished.
Thanks for the feedback