Suggestions for the BIOS setup:
Disable USB boot.
Disable auto IDE checking.
Disable floppy drive and floppy seek.
Make certain boot order has the HDD as the first (only?) boot device.
Enable quickboot (if an option).
For within Windoze:
Start > Run > MSCONFIG
Disable an components you don't want running at startup. With CF running as a shell, I'm not certain how this will affect anything.