The DDR controller initialization parameters defined in board/freescale/ls1043ardb/ddr.h in u-boot source code is only used for LS1043ARDB demo board, you need to use QCVS DDRv tool to calculate, optimize and validate DDR controller configuration parameters for your custom board.
Did you define ddr_raw_timing in board/freescale/ls1043ardb/ddr.c according to your DDR datasheet?
If yes, you could try the following method to create a QCVS DDR project to connect to the target board to do optimization and validation.
1. Please define CONFIG_SYS_DDR_RAW_TIMING in include/configs/ls1043ardb.h and rebuild u-boot. Then boot u-boot image on your custom board.
2. In CodeWarrior IDE, please create a QCVS DDR project, in "DDR configuration" panel, please select "From target" Configuration mode, after type CodeWarrior TAP IP address, please click "Read from target", then create the QCVS DDR project with parameters read from your custom board.
3. Please complete DDRv Centering the clock, Read/Write ODT and driver validation and Operation DDR tests.
4. Please click Project->Generate Processor Expert Code, please refer to DDR controller configuration parameters in file uboot_ddr1.c in Generated_Code folder to configure DDR parameters in board/freescale/ls1043ardb/ddr.h in u-boot source code.
I attached QCVS DDRv tool user manual.