This is working a bit better now:
This is just currently running the minimum 16kb rom starting at 0xc000, and I don't currently have turbo mode.
I changed things to use a 64MHz clock and power of 2 clocks derived from it including a 32Mhz clock for the VGA. I really need to change the vga timings to match that, but it works on my monitor without any changes.
I could probably make it work with the 25Mhz clock by reserving 8 cycles for the SDRAM access and 8 cycles for refresh.
I have not yet tried SD card access, but there should not be a problem with that.
I also have not tried audio of any IO other than VGA and the PS/2 keyboard.
This version does not need to be run from flash memory as I am waking up the flash memory correctly now.