@EricAnderson, did you happen to get anywhere with this? We have the exact same scenario. Our Consultant thought he had it working by doing the following, but now it appears it may not be working completely:
Made a UDF in the PO Detail file, used the sales order line sequence as the source, and passed that through to the PO.wrk file - and sorted off that. Will post further info as we get it.
The sad thing is that Ext Sol PO-1020 (http://www.sagesoftware.com/mas90/ext_solutions/files/PO/po-1020.pdf) had that option: ""Transfer S/O Lines Unsorted/Uncombined: Select Yes if you want the lines transferred from the Sales Order to appear in the same order on the Purchase Order.