Until you figure out the reason for the tunnel not coming up I have learned that instead of rebooting the device you can issue the following command to "kick" the ipsec renegotiation to bring the tunnel back up instead of rebooting.
From the cli: restart ipsec-key-management immediately
Note this will kick all tunnels, but they should come up quickly assuming you don't have a ton of tunnels.
Hopefully that keeps you from having to wait on JunOS to boot.