Firstly, welcome to the world of building guitar kits.
Yes you can fill holes - no problem and I would in that case. Either wood filler, glue or dowel and glue even body filler (bog). You just have to make a choice depending on how visible it will be and proximity to other holes etc. In your case the simple way that I would try would be timbermate or similar before you finish the guitar and drill the other holes as you can sand the excess Timbermate off easily.
I wouldn't worry about that crack. Once you use some Tru-oil of similar it will fill it just fine. Alternatively, superglue if you were really concerned.