Help, I can't access the file system on my nexus 7

[Bryon15]

Here's everything I did. My nexus 7 was and still is rooted. Anyway my nexus 7 had slowed down recently. So I was advised to reinstall the stock rom. So I backed everything up that was on it and installed the latest version of android (4.2.2). It worked. It's not slow anymore. I transferred the backup files back onto it. But now there's a big problem. I can't do anything with the file system using es file manager. I can't delete a file that's on there, I can't edit anything, I can't create a new file or folder, I can't download anything. I just tried to download the music video beat it by Michael Jackson from youtube using the tubemate app. It said: Error: open failed: EACCES (permission denied). I was told that i need terminal emulator and adb tool to fix it. But using them seems really complicated. I have no idea what I'm doing. Can anyone help me?