I unfortunately never was able to resolve the issue. I abandoned this track and am slowly replacing the 2TB drives with 6TB in which I'll eventually expand the pool for more storage. If you ever figure it out, I would definitely be interested in how you fixed it considering all the trouble it gave me!
Well I was able to resolve the issue and it had to do with the bios on my LSI 9211 card. It turns out that the mpt bios will screw up the boot sequence.
The solution was to reflash the LSI card with firmware but no bios.
Follow this guide
https://nguvu.org/freenas/Convert-LSI-HBA-card-to-IT-mode/
to make a boot drive and flash firmware except instead of doing
sas2flsh -o -f 2118it.bin -b mptsas2.rom
do
sas2flsh -o -f 2118it.bin
This flashes the firmware but no bios. You'll notice you don't get the LSA bios boot screen either. After the flash I was able to boot and add a 6 drive vdev to my existing raidz2 array. Note: A bios is only needed if you want to boot off a drive directly attached to the LSI card. If you want to boot from USB the MPT bios on the LSI card screws things up - so remove bios and life will be good.
Summary of steps:
- Remove drives until you can boot from USB
- Boot into usb drive that has firmware utilities
- Flash LSI card WITHOUT bios (follow guide but don't flash bios)
- shutdown
- Reconnect all drives
- Boot into freenas
- Put the pistol away