Thanks Keith,
After much frustration, my entire issue was I am a new to xpages and it was just a syntax issue on the csjs, so here is the actual code I have in the column for the on click event for csjs. I changed my ssjs function so I could pass the two variables I needed to build the link.
var li = "#{javascript:getARInvoiceLink2(arlist.getColumnValue("tx_orgid"),arlist.getColumnValue("tx_trxnumber"))}";
window.open(li);