At this time we are still running OE 8.1C and Receivables 9.0B - could this be the problem of the links not working?

I tried your suggestion anyway and this is the error I get on the Customer Number -> Customer no:
"The link you added causes a link configuration with multiple paths leading to the same table. You may want to cosider reversing the links."

When I try reversing the links I get this:
"Invalid file link. Not consecutive index fields."

When trying to make the link for Ship to address code -> Contact Code I get the same:
"Invalid file link. Not consecutive index fields."

For whatever reason if I only use the Territory from the OE table it does not bring in any customers who have subsequent Ship-tos which are stored in the AR90W Contact/Shipto table. Here is an example of this:

Shipping to Fred in Prince Albert (territory 6 - setup in - OE-Customers-Contacts/Shipto Tab)
Billing goes to Fred in Saskatoon (territory 10 - setup in - OE-Customers-Invoicing Tab)
Fred also has 3 other ship-to addresses in territories 4, 5 and 8 which also do not pull into the report.

I hope this makes sense?