run
sudo chown yourusername:yourusername * -R
again. seems you misused sudo once (or several times) ;-)

Hehe, I probably sudo'd myself to linux-hell.

Anyway, chown-ed again, same result:

me@ubuntu:~/yacoin/src$ make -f makefile.unix results in:
......................... boost_program_options -l boost_thread -l db_cxx -l ssl -l crypto -l miniupnpc -Wl,-Bdynamic -l z -l dl -l pthread
/usr/bin/ld: cannot open output file yacoind: Permission denied
collect2: ld returned 1 exit status
make: *** [yacoind] Error 1

When trying with
me@ubuntu:~/yacoin/src$ sudo chown me:me * -R

me@ubuntu:~/yacoin/src$ sudo make -f makefile.unix I get
/bin/sh ../share/genbuild.sh obj/build.h
..............................
boost_program_options -l boost_thread -l db_cxx -l ssl -l crypto -l miniupnpc -Wl,-Bdynamic -l z -l dl -l pthread
/usr/bin/ld: cannot find -lboost_filesystem
/usr/bin/ld: cannot find -lboost_program_options
/usr/bin/ld: cannot find -lboost_thread
collect2: ld returned 1 exit status
make: *** [yacoind] Error 1

This is getting annoying, appreciate your assistance.