With the addition of Run Customized, the run menu looks like

Python Shell
Check Module
Run Module
Run... Customized

This order resulted from Check and Run Module originally being implemented as extensions, which forced them to be below Python Shell.  The situation was similar with Format Paragraph being forced below less commonly used options on the Format menu.  It is now at the top.
Run... Customized was tacked on below, without worrying about the appropriate order for the menu..

On issue #37627, Raymond Hettinger suggested "Move the [new] menu option up by one so that the regular F5 "run" is last -- learners we having a hard time finding and mouse targeting the more commonly used regular "run" option.  The result would be

Python Shell
Check Module
Run... Customized
Run Module

I would rather make Run Module, the most commonly used option even more prominent by putting it at the top, perhaps by reversing the order.

Run Module
Run... Customized
Check Module
Python Shell

With Run Module at the top, remaining items could be ordered by logic, and to me, the above is plausible on that score, or by use, perhaps putting the second-most used at the bottom.  I suspect that this will be Run Customized.  To me, Check Module is useless, though I can imagine situation when it is not.  Python Shell is only needed when there is no shell and one does not want to make one appear by running a module.  To switch to an existing Shell, on should use the Windows menu.  Anyway, another candidate is

Run Module
Check Module
Python Shell
Run... Customized