hellomynameisphil

I also install my kernel manually. The process that I have been using for upgrading is very similar to your initial install...
 
# merge different or updated kernel package (e.g. gentoo-sources)
emerge gentoo-sources
 
#change /usr/src/linux link to the new kernel package directory
eselect kernel list
# find the number x corresponding to the new version
eselect kernel set x
 
#transfer old kernel config (e.g. 4.0.0. is the old kernel version)
cp -av /usr/src/gentoo-sources-4.0.0/.config /usr/src/linux/.config
 
#enter kernel directory
cd /usr/src/linux
 
#kernel config
make oldconfig
 
#optional - review/change kernel options
make menuconfig
 
#build and install - assumes that /boot is mounted if separate to /
#include -j8 so to use 8 threads (same as MAKEOPTS in make.conf)
make -j8 bzImage
make -j8 modules
make install && make modules_install
 
#update external initramfs (if applicable)
 
#update bootloader (assumes sys-boot/grub and correct /etc/boot.conf)
boot-update
 
#re-merge kernel module packages against new kernel (e.g. x11-drivers/nvidia-drivers)
emerge --ask --verbose @module-rebuild
 
After a successful reboot and verification of new kernel, consider removing old kernel files.
 
#old kernel source directory
cd /usr/src
rm -r gentoo-sources-4.0.0
#kernel files installed to /boot
cd /boot
rm vmlinuz-4.0.0
rm config-4.0.0
rm System.map-4.0.0
#old kernel modules
cd /lib/modules
rm -r 4.0.0

i dont know, i use ntpd...  
 
cat /etc/conf.d/hwclock
clock_hctosys="YES"
clock_systohc="YES"
 
mkultra@spaceball-1 ~ $ sudo /etc/init.d/hwclock status
* status: started
 
that makes the system read cmos time at start, and write cmos time at halt....  the kernel has some RTC stuff to do it also....  dig through the issue and start documenting solutions plz, im busy trying to figure out entropy stuff for ssl security.
 
"In-kernel method[edit]
On a sufficiently modern kernel (3.9 or newer), Linux can be configured to handle setting the system time automatically:
KERNEL
Device Drivers  --->
  [*] Real Time Clock  --->
    [*]   Set system time from RTC on startup and resume
    [*]   Set the RTC time based on NTP synchronization
The hwclock init script should not be ran when using the kernel's real time clock. Opting for this method will speed up the system's boot and shutdown processes slightly." -https://wiki.gentoo.org/wiki/Ntp
 
i did document sufficiently ntpd, the kernel entry is not mine though.
 
did that work for you?  if not you're probably going to have to change your clocks adjustment thing /usr/share/zoneinfo/America/Detroit
 
/etc/localtime -> /usr/share/zoneinfo/EST5EDT
 
uhhh for you its PST8PDT i think....

do you have ntpd or crony installed?  if so are they writing to the cmos at halt?