The linking to the contracts in Sage 300 is very choppy and the Prime Invoice data that posts to one contract line item doesn't provide useful information. There is no need to link to the contract or contract items in S300, if SCM can just link to and post to a job and send the contract info to the job, and the Prime Invoice to AR as it happens already. Just eliminate the contracts component. I am attaching a Word document with screenshots explaining this concept.
I believe we can figure out the Prime Invoice Line Item sort order portion of this document with hh2's help.