An older mrp system sitting on top of D3/Unix...

There is no standard entry routine handling user input for any of the
application entry screens (just a bunch of "INPUT Q", "INPUT ANS", "INPUT
someting else", etc.).

Is there a function/command that can be placed in either the account
defining item or individual USER file macro section that will force all
input to uppercase?

Not that I'm aware of - may be possible from Linux though

You COULD write a routine that scanned all source code, looking for

INPUT <whatever>

and changed to

INPUT <whatever> ; <whatever> = OCONV(<whatever>,"mcu")

However, I can see there are times that you would WANT to be able to
enter lower case
eg: a product decription of "Visage" rather than "VISAGE", so perhaps
you are best doing this on a case by case basis.

Given the fact that D3 is (by default) case insensitive, what is the
problem ?

Hmm, actually you probably could link something in using triggers ...
why not just manually change the areas that ARE causing concern ?