No offense, but you can easily remove the upper bolt without even touching the liner. Just because the shop manual says you need to do something doesn't necessarily mean that it needs to be done to complete the job. The liners are definitely not warped. Also if you read the rest of the thread, the bolts are not in backwards. Someone posted a picture of how the bolts should be installed and that is how mine are installed. There was initial confusion over how the bolts were installed based on a description of the direction of the bolts someone posted, but they are installed correctly.
I am definitely telling you "the whole story" as you put it. I'm not hiding anything or leaving anything out. If you guys need more information or details let me know and I'll be happy to oblige.
I appreciate everyone’s assistance and ideas.