Time out only will work if you are booting from the custom boot entry of clover.
After installing the clover to SSD, have you copied the config.plist file from your USB's /EFI/CLOVER folder to SSD's /EFI/CLOVER/ folder (on your EFI partition) ??
For timeout, on the clover boot loader screen, choose
Clover Boot Options and then choose the option
Add Clover Boot Option.
Then go to BIOS and set the boot.efi as you primary boot entry/device. Save the settings and the reboot. Your timeout will work.
Note:- If you are not able to see any clover entries in your BIOS's boot sequence list even after adding the CLOVER boot option manually, then every time you have to press enter key. It seems like bug in clover. I this problem in one of my build.
For enabling onboard Audio (ALC 885 - ALC1150) :
http://www.tonymacx86.com/audio/143757-audio-realtek-alc-applehda-guide.html
Post your org.chameleon.boot.plist file.
Post the screen shot of Applications > Utilities > System Information > Graphics/Displays.
Open Terminal and type the below command,
Then check for the section Intel Device Info, post a screen shot of the section.