09-25-2016
I think you have to work "backwards".
Change startup to be more minimal, do not start any your own daemons.
If the problem goes away, keep adding them back into the mix one by one. If it is resource contention, like waiting on some kind of lock, it may be hard to track down. Any daemons that work cooperatively with others may deserve first attention.
If the problem still exists, you may have to start looking at your configuration by changing to single user boot, then changing startup/shutdown script to boot and shutdown at each runlevel to eliminate process groups and processes as a problem.
I vote for your hand-rolled daemons as a great place to start. Sorry I cannot be more specific.
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reboot(8) System Manager's Manual reboot(8)
NAME
reboot - Restarts the machine
SYNOPSIS
/usr/sbin/reboot [-dlnq]
DESCRIPTION
When the system is running and multiple users are logged in, use the shutdown -r command to perform a reboot operation. If no users are
logged in, use the reboot command.
The reboot command normally stops all running processes, syncs the disks, logs the reboot, and writes a shutdown entry in the login
accounting file, /var/adm/wtmp.
The reboot command uses the sync call to synchronize the disks, and to perform other shutdown activities such as resynchronizing the hard-
ware time-of-day clock. After these activities, the system reboots. By default, the system starts and the file systems are automatically
checked. If the start-up activities are successful, the system comes up in the default run-level.
You must have root privileges to use this command. Using the -n flag can result in file system damage.
FLAGS
Generates a crash dump of the system before halting it. Can be used with any of the other flags. Does not log the reboot using syslog
Does not sync the disks or log the reboot using syslog Performs a quick reboot without first shutting down running processes; does not log
the reboot using syslog
EXAMPLES
To enable the default reboot action, enter: reboot This command causes the system to stop all running processes, sync the disks, log the
shutdown, and perform other routine shutdown and reboot activities. To shut down the system without logging the reboot, enter: reboot -l
This command shuts down the system and performs all shutdown and reboot activities, except logging the shutdown. To reboot the system
abruptly, enter: reboot -q This command reboots the system abruptly without shutting down running processes.
FILES
Specifies the command path Specifies the login accounting file Specifies the path of the syslog daemon
RELATED INFORMATION
Commands: fsck(8), halt(8), init(8), savecore(8) shutdown(8), syslogd(8)
Functions: reboot(2), sync(2), syslog(3) delim off
reboot(8)