Help Closet installation!

Hi, I am currently trying to install custom closet for my sons' room. My DH and I made the design ourself and bought the Completions collection from Closetmaid at Lowes. As I am tearing the exisiting shelf/rod out and there will be no doors, I took the board from the wall that kinda frames the closet. However, at the bottom now there is a gap in the baseboard where that frame was. I not sure of whether to replace the entire baseboard around the room, leave the gap there or just take out the closet baseboards and leave it bare. Any suggestions? Also, I have been filling in the nail holes in the walls, and just wanted to make sure that I am using the correct stuff. It is called plaster repair, but I have drywalls. Thanks for your help. --SAZ