Scaling with Waypoint System

I’m attempting to show flow through these pipes with a trail renderer attached to a sphere using the waypoints system. Everything was working properly until I went to build on the Hololens for the first time and realized the model was way too big. I tried adjusting the camera instead of the model but it was still too big. When I scale down the model itself, my waypoints system stops working as you can see in the photo, even thought they are child objects and the scale/transform doesnt actually change in the inspector (I guess it is world space, not local space).
Even when I replace the waypoints it still acts erratically. I know you should avoid scaling when it involves positional data, but I couldn’t really do it any other way. If anyone could offer any advice/ideas about how to fix this issue I would greatly appreciate it. I have a deadline coming up to have this built on the Hololens.