Handwriting mathematics, and handwriting in general, I find are two different things. It's especially obvious for me because writing actual words hurts my hand relatively quickly and writing math, even pages upon pages of it, doesn't.
To get better at writing math, I practiced specific symbols, changing some letters from my 'standard' handwritten form, to make them much easier to distinguish: I changed my
y to be two-story, my
x to be made of curved parts, my
t to have a tail, my
v to be very sharp and my
u to have its tail quite long. This of course has its own history even in "official" mathematical symbols: see for instance $\ell$ as opposed to $l$.
Most of the time nobody cares about the sizes of things. If you find a particular size too small to comfortably or readably write (and this of course can depend on things like the writing utensil and medium), write bigger! It doesn't matter where it is. The fourth superscript can safely be the same size as the thing you're putting the tower of superscripts on and as long as the position is sensible it will be understandable. (this doesn't apply to "large operators" - $\int$ and $\sum$ et al do benefit from large size).