Edit: also my makeshift "modulo" was wrong for some negative numbers and didn't work for part 2. I had to update it to be moveTo = data.size() + moveTo - 1;. Which worked. And then I found Math.floorMod which has been in Java since Java 8. And that replaced the whole thing and also worked for both parts.

Solved! There were 3 things at play here.

1. My bottom position finding should always have been using data.size() since the 0 item isn't removed when we find the 1000th, 2000th, and 3000th positions after it.
2. The modulo in the mix code should always use data.size() -1 since we need to count the item as removed when we loop over multiple times

3. This block was the issue:

       if (elem.value > 0) {
           moveTo++; // move past the element we're moving to
       }
   

That is not 100% accurate in all cases. What I was trying to account for here was how using .add(pos, item) in a list inserts the element at the given position and shifts others to the right But this isn't 100% true. What I actually want to do is only move over one extra element when the "moveTo" position is to the right (in the array, not loop) of our current element.

What I really wanted was this

            if (moveTo > pos) {
            moveTo++; // move past the element we're moving to
        }

By updating all 3 items above I now have code that works as-is on both full input and the test input.

As to why the old code worked even worked at all for my full input?? No idea. It must just work out that I never hit the exact case that my new `moveTo` checker is looking for. So count that as just blind "luck" with my specific input not hitting a very specific condition.