It looks like the Nios2 Makefile was patched multiple times.
You should do the nios2 patch only once.
Try rename the old uCLinux-dist-test tree, and create a new one .
Then compare what is changed in Nios2 Makefile.
If you want to config kernel, you should be in ~/uCLinux-dist-test dir, and
make menuconfig
Kernel/Library/Defaults Selection --->
(linux-2.6.x) Kernel Version
(None) Libc Version
[ ] Default all settings (lose changes)
[*] Customize Kernel Settings
[ ] Customize Vendor/User Settings
[ ] Update Default Vendor Settings
Then <exit> <exit> <yes> .
It will enter kernel config.
And after you finish kernel config,
make linux image