Welcome to the FJR. Yours is not a unique question. Here is a link to the last thread on the subject:
https://www.fjrforum.com/forum//index.php?showtopic=12233
Because you are in Canada . . .
Hide the red key and make sure you have the key code tag (just in case, but if you ever mess it up THAT badly, that you have NO keys you'll be in trouble anyway - that red key is the master programming key. Without it you can't teach a key to the immobiliser.
The clear stick-on tells me your bags weren't mounted properly - there are 6 pieces of clear stick-on provided with the bag kit. The manual provided with the bag kit says where they all go. Check the torx screws at the rear of the locks to make certain they used blue loctite on the threads.
I didn't see you list the cheesy tool kit.