Well, finally i was able to fix it.
- the tool configure.ac file was not written in account to using libusb-compat (but for only libusb-0.1).
So i solved it by adding dependency while searching libusb-0.1 (-lusb-1.0):
AC_CHECK_LIB([usb], [usb_get_string_simple], [have_libusb=yes], [], [-lusb-1.0])
2. Another problem was to make AC_CHECK find libs not in standard system /usr/local/lib folder as modified library interface was a bit different and it tried to gcc with system one while searching with AC_CHECK_LIB. I used CPPFLAGS to set the right libs path