Upgraded 14.04 to 16.04 and boot is dropping to initramfs prompt

Question

Anyone know how to fix this? I upgraded a system with LVM partitions for /, /var, /usr, /home and it seems like initrd can't figure out the LVM scheme. I found a bugreport on launchpad regarding this issue however applying the activate VGs when root=UUID= patch on that page does not fix it. If I run vgchange -a y from the (initramfs) prompt, I can mount the partitions but not sure what else to do at this point.

Begin: Mounting root file system ... Begin: Running /scripts/local-top ... lvmetad is not active yet, using direct activation during sysinit
done.
Begin: Running /scripts/local-premount ... done.
Begin: Will now check root file system ... fsck from util-linux 2.27.1
[/sbin/fsck.ext4 (1) -- /dev/mapper/vg_new-slash] fsck.ext4 -a -C0 /dev/mapper/vg_new-slash 
/dev/mapper/vg_new-slash: clean, 20787/262144 files, 447481/1048576 blocks
done.
[ 2.154404] EXT4-fs (dm-0): mounted filesystem with ordered data mode. Opts: (null)
done.
Begin: Mounting /usr file system ... [ 2.318500] tsc: Refined TSC clocksource calibration: 3399.996 MHz
[ 2.319741] clocksource: tsc: mask: 0xffffffffffffffff max_cycles: 0x31024b3bec5, max_idle_ns: 440795366697 ns

Begin: Waiting for /usr file system ... Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... [ 26.329688] random: nonblocking pool is initialized
done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
Begin: Running /scripts/local-block ... done.
done.
Gave up waiting for /usr device. Common problems:
 - Boot args (cat /proc/cmdline)
 - Check rootdelay= (did the system wait long enough?)
 - Missing modules (cat /proc/modules; ls /dev)
ALERT! UUID="78933db3-c0e9-466d-8855-4c5b0806244f" does not exist. Dropping to a shell!

BusyBox v1.22.1 (Ubuntu 1:1.22.0-15ubuntu1) built-in shell (ash)
Enter 'help' for a list of built-in commands.
(initramfs) 

UPDATE: Tried several things including various SF posts, but in the end, had to issue vgchange -a y by hand and then exit the initramfs prompt which appears to have finished booting the system. It's running but still wounded as a this has to be done at every reboot.

...
(initramfs) vgchange -a y
  /run/lvm/lvmetad.socket: connect failed: No such file or directory
  WARNING: Failed to connect to lvmetad. Falling back to internal scanning.
  6 logical volume(s) in volume group "vg_new" now active
(initramfs) ls /dev/vg_new/
slash      swap       usr        home       var        mysql.bak
(initramfs) exit
Begin: Will now check /usr file system ... fsck from util-linux 2.27.1
[/sbin/fsck.ext4 (1) -- /dev/mapper/vg_new-usr] fsck.ext4 -a -C0 /dev/mapper/vg_new-usr 
/dev/mapper/vg_new-usr: clean, 100849/655360 files, 532430/2621440 blocks
done.
[   95.723025] EXT4-fs (dm-3): mounted filesystem with ordered data mode. Opts: errors=remount-ro
done.
Begin: Running /scripts/local-bottom ... done.
Begin: Running /scripts/init-bottom ... done.
[   95.820637] systemd[1]: RTC configured in localtime, applying delta of -360 minutes to system time.
[   95.842471] systemd[1]: systemd 229 running in system mode. (+PAM +AUDIT +SELINUX +IMA +APPARMOR +SMACK +SYSVINIT +UTMP +LIBCRYPTSETUP +GCRYPT +GNUTLS +ACL +XZ -LZ4 +SECCOMP +BLKID +ELFUTILS +KMOD -IDN)
[   95.845583] systemd[1]: Detected virtualization qemu.
[   95.846601] systemd[1]: Detected architecture x86-64.

Welcome to Ubuntu 16.04.5 LTS!

[   95.851545] systemd[1]: Set hostname to <myhost>.
[   95.946468] systemd[1]: usr.mount: Unit is bound to inactive unit dev-disk-by\x2duuid-78933db3\x2dc0e9\x2d466d\x2d8855\x2d4c5b0806244f.device. Stopping, too.
[   95.967000] systemd[1]: Reached target Encrypted Volumes.
[  OK  ] Reached target Encrypted Volumes.
[   95.969414] systemd[1]: Listening on LVM2 poll daemon socket.
[  OK  ] Listening on LVM2 poll daemon socket.
[   95.971863] systemd[1]: Created slice User and Session Slice.
[  OK  ] Created slice User and Session Slice.
[   95.974105] systemd[1]: Listening on /dev/initctl Compatibility Named Pipe.
[  OK  ] Listening on /dev/initctl Compatibility Named Pipe.
...