I had the same issue with the clock, you need to got Settings > CyanogenMod Settings > Interface > Status Bar tweaks. Set the clock color and then dis-enable and re-enable it.
For the stock navigation app, someone is bound to have it has a flashable zip, but I don't.
Thanks that worked great! Two more questions.
1. How do I get my voicemail to work correctly I keep getting the 9016 text.
2. In the past I had a microphone on my keyboard for speech recognition. How do I get that back?