Hi Terry,
The problem you're encountering with na_ide_ide errors is fairly common and will be rectified in the next release if all goes well.
I'm going to get one of our hardware guys to answer your question regarding the compact flash interface because I'm really not to sure about the specifics. At a high level, there is a compact flash SOPC component that can be included in your design that works with the driver provided in the Nios II Linux distribution. Once that is built into your hardware design the kernel should build alright.
Alternatively, in the kernel, you can always disable the ATA/ATAPI/MFM/RLL support, but I'm guessing you want compact flash support.
http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/smile.gif
Expect another response soon.