Charging system over charging?

From Manual
https://wranglertjforum.com/attachments/2006-tj-service-manual-pdf.14047/
DIAGNOSIS AND TESTING - CHARGING SYSTEM The following procedures may be used to diagnose the charging system if: • the check gauges lamp (if equipped) is illuminated with the engine running 8F - 22 CHARGING TJ • the voltmeter (if equipped) does not register properly • an undercharged or overcharged battery condition occurs. Remember that an undercharged battery is often caused by: • accessories being left on with the engine not running • a faulty or improperly adjusted switch that allows a lamp to stay on. Refer to Ignition-Off Draw Test in 8, Battery for more information.

INSPECTION The Powertrain Control Module (PCM) monitors critical input and output circuits of the charging system, making sure they are operational. A Diagnostic Trouble Code (DTC) is assigned to each input and output circuit monitored by the On-Board Diagnostic (OBD) system. Some charging system circuits are checked continuously, and some are checked only under certain conditions. Refer to Diagnostic Trouble Codes in; Powertrain Control Module; Electronic Control Modules for more DTC information. This will include a complete list of DTC’s including DTC’s for the charging system. To perform a complete test of the charging system, refer to the appropriate Powertrain Diagnostic Procedures service manual and the DRBt scan tool.

https://wranglertjforum.com/attachments/2006-tj-powertrain-pdf.14050/
Perform the following inspections before attaching the scan tool. (1) Inspect the battery condition. Refer to 8, Battery for procedures. (2) Inspect condition of battery cable terminals, battery posts, connections at engine block, starter solenoid and relay. They should be clean and tight. Repair as required. (3) Inspect all fuses in both the fuseblock and Power Distribution Center (PDC) for tightness in receptacles. They should be properly installed and tight. Repair or replace as required. (4) Inspect generator mounting bolts for tightness. Replace or tighten bolts if required. Refer to the Generator Removal/Installation section of this group for torque specifications. (5) Inspect generator drive belt condition and tension. Tighten or replace belt as required. Refer to Belt Tension Specifications in 7, Cooling System. (6) Inspect automatic belt tensioner (if equipped). Refer to 7, Cooling System for information. (7) Inspect generator electrical connections at generator field, battery output, and ground terminal (if equipped). Also check generator ground wire connection at engine (if equipped). They should all be clean and tight. Repair as required. SPECIFICATIONS GENERATOR RATINGS TYPE RATED SAE AMPS ENG

Mine doesn't get anywhere near 15V. I'd put a known good meter on it before you dive too deep. What does a battery smell like when it is overcharged?

I'd put a voltmeter on the battery, sounds more like you have a ground issue or like you say, bad connection to the ecm.

If your PCM is working correctly and your volt meter is correct you should be getting a P0563 codes if the the voltage is 1 volt over target 13.47 v. I would give WranglerFix a call.