Its nothing unusual, its 6 volt Positive Ground with a simple Cutout Relay and a Low High Charge control switch system that the gennys FLD post wires to. See how she charges if you momentarily jump the FLD post to ground?? If she charges fine then but not otherwise,,,,The Low High charge switch is bad,,,,,,,or,,,,,,,,,,,The LH switch isnt well grounded,,,,,,,or,,,,,,,,,,,the wires open from FLD on Genny up to the LH switch.
A good charged battery should read around 6.3 volts just sitting there engine not running, but if coupled to a good working genny at high RPM the battery voltage should rise to at least 6.5 up to 7 + volts. That 5.5 sounds like a bad genny and/or mis wiring or a short.
On HIGH charge the wire leading to the Gennys FLD post should be an effective dead short to ground and at Low charge approximately 3 or so ohms is inserted between frame ground and the FLD post. If the LH switch isnt well grounded, that can cause non charging since theree no current path for field current INSURE LH SWITCH HAS A GOOD GROUND
You can bench test the Genny using my Motor Test in my URL link below. For a detailed step by step troubleshooting procedure for non charging run through it and post back any questions