Convert all indexing variables to `size_t`/`ptrdiff_t`

Currently many of the indexing variables we use are of type 'int' when they should be size_t (or ptrdiff_t if they're a difference). This could potentially lead to issues with the range of int as the size of VRAM on GPUs grows and this change would allow us to enable the following clang-tidy checks:

• bugprone-implicit-widening-of-multiplication-result
• bugprone-narrowing-conversions (alias of cppcoreguidelines-narrowing-conversions)

This conversion wouldn't be too difficult but would be time consuming and would be a good project for a new student/collaborator to become familiar with the code.

See this discussion for the original discussion on the topic.