[EDIT: solved. See post below.]

I just installed a new IMA battery. Everything seems to have gone fine, and the car started up using the IMA a couple of times. But, it refuses to engage the IMA system while driving.

I did disconnect and reconnect the 12V battery terminal. I also revved the engine at 3500rpm for 75 seconds, then idled for 60 seconds. I tried driving, then starting again and it didn't help. It was supposed to switch to 4 bars instead of zero and update.
I also drove it around for over 30 minutes straight (per the Manual). Every time I hit the stop sign the red battery light came back on. It made no difference at all, the indicator still shows zero bars of battery charge.

The check engine light stubbornly comes on. The red battery light is also on, but it goes away when I rev the engine. When I clear the engine codes using a code scanner, they blink off then come right back. I scan for codes immediately after clearing them and they're the same:
P1600, P0A80 (Generic IMA code, Replace IMA Battery)

My IMA system is behaving the same as before I changed the battery: It refuses to charge or power with the IMA. So, other than starting up using the IMA starter, it refuses to use the IMA battery for anything. So, I have no way to recharge it. (It should have plenty of charge after being shipped to me from the factory.)

I think I wound up with 2 extra 10mm hex-head screws after I re-installed. I do have the screws on the ground wire and the metal clip at the top of the battery. Also the metal plate over the on/off switch is screwed on. So, I don't know where those 2 came from.

Also, I didn't reinstall the rear seat back yet because I wanted to verify it works before covering it up. I do have all the T30 bolts securing that metal plate.

The only other thing of note is the DC/DC plug on the battery case they shipped me was cracked, so it didn't attach to that lip on the battery. It hangs loose, but the connection seems fine. They told me that shouldn't be any problem for the battery to work correctly.

 

Problem solved.

I got ahold of Greentec Auto, who I bought the battery from. I needed to cut a bypass line. It was a red loop at the top-left of the battery (right behind those 3 plugs). Apparently that wire has to be cut if you have newer software.

So far everything seems to be working fine.