Stu released a Type 6 board (still beta/prototype) to nistune your stock ECU (in the past had to be a Z32 8-bit ECU)
There was a thread started in this forum, however r31nismod decided to delete it because it sounded too much of a trader ad.
You should speak to Mat from Nistune, he might have a solution for you retaining your factory ECU, however with the new type 6 nistune board.
I, myself have not used (type 6 that is) however it looks very promising, have however used/tuned other nistune vehicles and it's great.