Just sharing my suggestions....
>> It appears that there was some customized install during the chroot environment we were unable to overcome
Possible to describe a bit on "customized installation" please?
>> The upgrade was difficult due to the chroot environment, and specific componentents not being located where scripts expected them to be.
I am sorry but can't understand "due to the chroot environment" part. :-)
May be little explanation will help.
>> "I've moved the trust relationships, however they aren't showing in the interface. The biggest issue I'm having now is the original DN's id is: @!13A3.08A9.8106.3629!0001!80A5.E1DE and the lab server can't change it's ID
Actually, we don't need to think much about Trust Relationship's DN's id ( or, `inum`, we call them ). Because, SAML transactions doesn't rely on inum but application and Gluu server communicate with `entityID` value.
So, best route would be.. just create those Trust Relationships again in new 4.x Gluu Server. You will just need to collect those SAML SP's metadata from old server `/opt/shibboleth-idp/metadata/` location.
>> When I imported users, they imported, but once I wanted to actually use them, I couldn't because the original DN's didn't match.
Are you using User's `inum` ( DN id ) for any kind of production operation? If not then we also don't need to bother those inums as well.
You can actually _pull_ those users from old server into your new server by using [Cache Refresh](https://www.gluu.org/docs/gluu-server/4.3/user-management/ldap-sync/) feature.