Make sure you have the MSCR_FLEXBUS and MSCR_SDRAM registers set to the right values. These registers ARE NOT DOCUMENTED PROPERLY. They perform the same "drive-level adjustment" as all the other "drive level" registers do and act the same way. They've just given the registers and the bits in them poor names that don't properly describe what they do.
Read the following for details.
https://community.freescale.com/message/66438#66438
https://community.freescale.com/thread/66541
Make sure your "split bus setup" is properly done, including the registers involved with this.
Download *ALL* the development board schematics. I have at least three for three different development boards, and I know Freescale has a fourth one they used internally. Representative file names (for searching):
POSREFDESIGNSCH.pdf
http://cache.freescale.com/files/soft_dev_tools/hardware_tools/printed_circuit_boards_for_reference_...
MCF5329_REF_DES.zip
1001664B_MCF5329_Schematic.pdf
Compare all the bus signals with what you've done. Especially the byte-lane selects, they're easy to get wrong.
On reflection there's another thing you should check:
> & from processor through buffer (level shifter) to flash.
"Level shifter"? It is a lot easier if you use FLASH that uses the same VCC that the DDR does.
Do you have the same "level shifter" in the data bus from the FLASH to the CPU?
I'm guessing you copied the "POSREFDESIGNSCH.pdf" which has shifters everywhere. Make sure the bus-direction-control signals are working properly.
You should be able to load some test programs (that you write yourself) into the Static RAM that can try some simple SDRAM and FLASH tests over the bus to try and isolate the specific signal problem you're having. At the least you can have that program in a loop running bus cycles so you can look at the signals with an oscilloscope.
Tom