I am trying to work a variant of this problem.

Two of us are already ticketed, in September,
AUS-MIA-LIM-IQT and IQT-LIM-LAX-AUS,
Business Class, the long legs on LAN for better seats.

We used 60K AA miles, as BA insisted they could
not include the LAN Peru legs LIM-IQT-LIM, nor could BA
come even close to the availability AA had open.

1) I hope to add LIM stopover on return.

At ticketing deadline, AA said LIM stop not possible.
I hadn't studied the rules enough to know.
Maybe convert to open jaw, buying IQT-LIM one way?
Likely to suffer a change fee, oh well.....,

2) IF that is doable, would try a separate business ticket,
preferably using BA miles, for LIM-SCL-IPC-SCL-x-LIM.

Some experimenting I did on BA.com surprised me,
needing less BA miles for LIM-IPC-LIM than SCL-IPC-SCL

Anyway, we will be slowly working a similar problem as OP.

Thanks for getting this thread alive,
and hope we can share solutiions along the way. @:-)