Yes it's choppy no matter what with iTunes, Google Chrome, YouTube. Both the front and the back have the same issue.
Which Mac are you pretending to be in your smbios? I've found that the iMac and MacMini options tend to generate a pop at the start of any audio. MacPro options sound better. However, on my Z87X-UD4H board, I've only been able to boot with MacPro3,1 and MacPro6,1 (which isn't accurately identified by the OS yet). If you're not sure how to create a smbios.plist file, check out Chameleon Wizard.
If you do alter your smbios file, be careful and make sure you have a bootable backup. As I mentioned, you can end up being unable to boot. Your system may experience other anomalies, for instance all my VPN settings go away because the OS thinks I've booted on another computer. This could also affect iTunes authorization. It's best to play with this stuff before you get too deep into iCloud and iTunes. There may be easy ways to deal with this, but I don't know what they are!
For easy testing, you can create multiple smbios.plist files to try in you /Extra folder, while keeping the original file untouched. For instance, create a test file with MacPro3,1 settings and name it smbiosmp31.plist. When your bootloader opens, type SMBIOS=/Extra/smbiosmp31.plist . Just this once, the system will boot with the smboismp31.plist file. If, after extensive testing you find it works great, you can backup your original smbios.plist and rename the test one to smbios.plist so it will load automatically at boot.
Also, there's no shame in buying a USB audio adapter that's Mac OS compatible and never worrying about sound again.
Good luck.