The DDR Initialization section provided in LS1046ARDB Target Initialization file is not suitable for your custom board, you need to modify DDR controller configuration section according to custom board.
You could use QCVS DDR validation tool to do validation and optimization to get the optimized DDR controller configuration parameter. Please refer to the attached QCVS DDR user manual.
1. Please create a QCVS DDR project with reading from SPD method.
2. Connect QCVS DDR validation tool to the target board to do validation and optimization, please refer to "1.2 DDR validation" in the attached document.
3. After validation, click project->Generate Processor Expert Code, then refer DDR configuration in ddrCtrl_1.py under Generated_Code folder to modify "DDR Initialization" in CW initialization file.