A spinal implant tool set includes end guide tools having flexible back wall flaps that receive opposite ends of the rod and intermediate guide tools that hold the rod in intermediate locations between the end guide tools. Both the end and intermediate guide tools include an attachment structure for operably connecting the guide tool to a bone screw. A multi-function installation tool and a bone screw driver each mate and cooperate with the guide tools. A method utilizing the tool set allows a surgeon to percutaneously implant the bone screws and the rod in the patient.