@eishiya I've just tried to offer possible solution regarding overall impression of the whole scene. It's not properly detailed edit and I agree that there's room for further improvement, I just didn't had more time for it. Feel free to edit it further.
@startselect
1. I would say practice with proper references is best approach. It's enough to draw one plank or beam of wood properly would bring you better understanding of wood structure for your second drawing. You don't even have to draw it with purpose of directly using it for a game, just draw it on it's own as a form of preparation and then try to apply that to the scene. As @eishiya said different details or characteristics may be disregarded in different situations to make it work for specific perspective, size, distance from watcher etc. so you should mostly have idea how texture should look and then find a way to make it work.
My wood edit is mostly on the door and even that is not very carefully done, everything else is just removing the noise and smaller details.
Pixel art is form of compressing visual information while still keep it recognizable. Learning from other pixel drawings may give you some hints of how some things can be handled but I think you will learn much more by trying to replicate actual photo reference. Even if you "fail" don't worry, just try again it will be better.
2. Honestly I didn't do any special, just played with colors a bit to make it work. @eishiya explained hue-shifting so I would just additionally recommend testing it out in different occasions and after some time you will get used to experiment with bigger color shifts. I've learned it over time and I can't say that I know ton of things about color, it's a very broad topic and for me true masters are traditional painters cause there's no color adjustment option there, with digital you can always change and adjust until it looks right without any harm to the piece.
If you are not sure how to start, even if everything sounds quite simple, you can sample colors from drawings you like and look at color wheel or color "square" to see where those colors are approximately and analyze it, after some time you will see some pattern in all greatness.
Also there's never a right way, you will find your own approach.