Techniques for implementing and/or operating a pipe handling system that includes an inboard bore plug assembly and an outboard bore plug assembly, which facilitate plugging a pipe bore in a flexible pipe. The inboard bore plug assembly includes a first inflatable plug having a first inflatable bladder that defines a first fluid cavity and a first inflation port opening and a first inflation fluid port secured within the first inflation port opening. The outboard bore plug assembly includes a second inflatable plug having a second inflatable bladder that defines a second fluid cavity, a second inflation port opening, and a bore port opening, a second inflation fluid port secured within the second inflation port opening, and a bore fluid port secured in the bore port opening to enable the pipe bore in the flexible pipe to be pressurized to an elevated fluid pressure.