in fact, try this. It works for me every time when i have to reinstall my VM. Starting from the root directory you checked out the project to eg. ~/navcoin2/
sudo apt-get install build-essential libtool autotools-dev automake pkg-config libssl-dev libevent-dev bsdmainutils libboost-all-dev
sudo add-apt-repository ppa:bitcoin/bitcoin
sudo apt-get update
sudo apt-get install libdb4.8-dev libdb4.8++-dev libzmq3-dev libgmp3-dev libminiupnpc-dev
rm -r src/obj
mkdir src/obj
mkdir src/obj/crypto
mkdir src/obj/support
sudo chmod 755 src/leveldb/build_detect_platform
rm -r src/secp256k1/
cd src
wget www.navajocoin.org/files/secp.zip
unzip secp.zip
cd secp256k1
sudo chmod 777 *
./autogen.sh
./configure --enable-module-recovery
make
cd ..
make -f makefile.unix clean
make -f makefile.unix USE_UPNP=1
If this works for you, I will update the linux build instructions.