modify factor_spu/config.h for different algorithm and/or number size.
#define SEARCH_FACTOR sets which algorithm to use
#define USE_SIMD uncomment to use unsinged long longs
#define NUM_SIZE how many quadwords are used for number (max value is 32)
number to be factored is set at the bottom of factor_ppu/ppu.c
after checking out you may have to fiddle with project setting in eclipse to get it compiling.
if you can't get it to work then ask (maybe i messed something up).