Item Substitution

My company deals in textile manufacturing with production facilities in
several US and foreign locations.  

My dilemma:

We need the ability to substitute based upon manufacturing costs -
lowest to highest.  We set up substitution records based upon costs
however, these items are 'hot' and rarely in stock at order entry time.
Allocations are run for the order(s) as a matter of course.  Since there
is no stock...no allocation records can be built.  Our Order Service
folks have indicated that if the allocation program is re-run for the
orders once there is stock available, the substitution scenario does not
work properly and cost info is skewed as the entered item seems to be
the selling item.  Chicago is telling us this functionality may be in a
future release of BPCS but, we need help now.  Has anyone worked with a
similar situation and, if so, how horrible are the modifications
required?

Thanks for any assistance,  

Deb Newcomb-Burke 
IT Director
Alba-Waldensian, Inc.