It's the other way round , a 749S front pipe hits the deep sump on the 999S engine. The 999S pipe will fit either model , the pipe just takes a route to the L/H side under the engine to avoid the sump (if fitted to a 749S it has nothing to miss)
ECU from 999S system will not work on a 749S , just leave the standard one on and get your dealer (hopefully a different one to the balloon who thinks the pipe will not fit
) to adjust the Co2 to suit , sorted