Have had some success so thought I would share the method. 

1)Make a BIN of the game 
2)Open up the BIN in your favorite HEX editor 
3)search and replace the following strings: 

NTSC -- 0100052402000624 

PAL -- 0100052403000624 

(so if you wanted to go PAL->NTSC you would search for the PAL string and replace it with the NTSC string) 
4)change vmode value in system.cnf to this: 
VMODE =NTSC or VMODE = PAL 

(note that the important thing here is to make sure that you re-insert the same number of characters that you delete,otherwise you get a BIN file with screwed block size) 
5)Burn. Your game should now be converted.