Joseph,
> Is there any specific order in which the Custom Fields are supposed to
> show up on the screen? I'm asking this question because every issue
> seems to show the fields in a different order, and the order does not
> necessarily reflect the order in the table.
Yeah, it should sort the custom fields by their rank (in ascending
order). Go to 'Administration -> Manage Custom Fields' and set the rank
on each custom field to make it sort correctly.
> Is it possible to customize the display of the fields to show
> different groups of fields in different colors?
>
No, that feature doesn't exist.
--Joao