Did you eliminate the voltage regulator on the firewall as part of the conversion? If so, the ARM wire and the BAT wire at the regulator should have been spliced together. Does the truck have an ammeter or an idiot light "NO Charge" indicator?
Yes, you can run a temporary wire (10 GA or larger) from the back of the alternator to the battery cable connection at the starter to get the battery charging, but you really need to wring out the wiring soon. Be sure to insulate the big wire you remove from the back of the alternator- - - -it could short out and cause problems. Don't cut anything away, just tape the connector off for now.
Jerry