Hello Michael,
the current mainline kernel support most of the features in Freescale 2.6.35 downstream kernel.
I suggest to use the Linux 4.1 because it will get longterm support in the near future.
In case you want to migrate from the old downstream kernel, you will need to build a new BSP for the custom board based on Device Tree.
Since your design bases on EVK you could copy arch/arm/boot/dts/imx28-evk.dts and modify it.
Regards
Stefan
Hello Jörg,
our problems result from using an old/wrong bootloader as we made there some changes due to our requirements. So to all who want porting to a newer 3.x/4.x kernel the advice take the appropriate bootloader.