I flushed the coolant system, and the cap looks like it needs to be replaced, the rubber was cracking. Also, I loosened the bleeder nut by the thermostat, and then eventually removed it completely, but the coolant didn't weep out as described in the manual. So, I started it and let it run for a few minutes, and the coolant started backing up into the overflow reservoir. So it looks like the thermostat is not working correctly. I am going to take into the dealer, and see if any other damage was done.
This was a process that I was trying to work through, and get some help from the forum. Thank you to the people that helped. Hopefully, someone down the line will be able to look at this, and figure out where to start, and what not to do. I should have started with the cooling system, and not with the tune.
Hopefully, I didn't damage anything.