Derek,
I appreciate you trying to diagnose my problem. I did bypass the clutch and tried to preform ready mode with no luck. Luckily, Rob at Fortin was able to help! Flash link was updated in October and now boots up automatically in wizard mode according to Rob. In wizard mode it won’t allow you to toggle from bypass mode to remote start mode because it’s supposed to do both when it gets flashed. Rob said this wouldn’t have been an issue if my car was an auto, or if I had a RF remote with a remote start button, because the unit is defaulted into ready mode 1 for manuals. He informed me I had to change some remote start settings and to do that I need to hit the above tab gear and put flashlink into pro mode. This allowed me to access the remote start stetting normally found under remote start mode. I then changed ready mode to option 2 because I’m using the factory remote and we verified some other setting. After that I was able to put the unit in ready mode and the vehicle started using 3x lock. Hope this helps other installers.
Andrew