Did you put in the deadzones?
That is the single most important step that prevents this problem as the autopilot in MSFS is very susceptible to signals from a controller that is close, but not 100% on dead center when released.
If you have done that and no luck, what are you using for a throttle?
The waypoint change is an issue, some waypoints can and some can’t.
Generally STARS waypoints wont.
There are numerous posts on this.
Do a search for “787 waypoints” to get some input.
Right now, there is an issue with icing which is preventing the planes from climbing properly
see this thread:
Do yourself a favor, get the just released stable version of the mod for the A320 and use that.
It is quite good, and not that hard to learn.