From what I've seen with the SST stuff it's been a hit and miss proposition depending on the bike. We were very happy with the exact combo you talk about on an 03 RM125 but I know others haven't been as thrilled with the results on various 250's.
probably a powercore 2. the shorty is designed for lower end power. (i think) well its supposed to be for tigher supercross style tracks. the powercore 2 gives you an increase across the whole powerband.
I have the SST/Powercore2 on my 03RM250 (EG265 Mo-Better Porting) and found it to have more torque and over-rev than the Fatty it replaced. Sorry, I can't comment 1st hand on your 01.