I had this problem as well and was ready to scratch my eye balls out. The fix is so stupid easy it will make you want to punt a puppy.
First delete all you have done and start from scratch.
git clone https://github.com/bitcoin/secp256k1
git clone https://bitbucket.org/shellnode/shell
First build libsecp256k1
./autogen.sh
./configure
make
./tests
sudo make install
sudo ldconfig
LD_LIBRARY_PATH=/usr/local/lib
export LD_LIBRARY_PATH
The last three commands are the ones that make the magic happen.Next, lets build Shell
I had to chmod my build_detect_platform file soooo....do this.
cd /src/leveldb
chmod +x build_detect_platform
qmake
make
or for headless
cd src
copy /shell/src/crypto folder to /shell/src/obj
make -f makefile.unix
Hope this helps. Still kind of a linux newb...