I have no problem dealing with developers, I just wish they would "up their game".
Last week, a piece of code that loops(!) through a bunch of records to insert...

I forgot about that one. I just put up with that fun myself.

SQL Server service account needs access to the folders where the data and log files reside, as well as the binaries. 
His account was probably an admin level account.

If he did that, please do not refer to him as a DBA!  It's an insult to those of us that are!

Aside from the two places you thought...

You cannot restore a SQL 2016 database to a SQL 2012 server.
You can re-create an empty database on 2012, and transfer the data into it from 2016.  There are...

For starters, your max memory setting needs to be adjusted.  

https://www.sqlskills.com/blogs/jonathan/how-much-memory-does-my-sql-server-actually-need/

Secondly, what is happening at the VMWare level?  Are there snapshots happening?  How is...

Another great day.  
Moved the production reporting server database to a new box Saturday

Weeks ago, the dev and QA instances were upgraded to SQL2014 SP2.  No bad...

I think it may make sense for you to do some learning.

Grant Fritchey wrote this article.
https://www.simple-talk.com/sql/performance/execution-plan-basics/

He has also written a good book.

This looks like an estimated plan, not the actual plan. 
Can you post the actual plan? 
The only thing that stuck out was that, even with 20+ indexes, the optimizer...

You have a new server.  You expect it to be fast, because it's new?

Have you looked at:
1. The configuration of the VM.
   a. How are the...

It sounds as if there may be rights granted to the second table that you may have missed. 

See if you can spot where the permissions were granted by...