Do you need to visit LHR twice?

If you wanted to drop in India you could route MAD-DOH direct. This will free up a segment and you could do HEL-DEL-NRT at the end. The HEL-DEL flights aren't daily so you will need to make sure they fit in with your plans.

I see what you mean about the AKL-SCL flights not showing up on the RTW tool even if EF shows D availability. I only found one flight that worked over a 3 month period.

Do you really want to route KUL-DRW on a 737? Might be better off going to BNE or PER from KUL and then on to DRW? Beware though the DRW PER flights don't run every day.

I priced up an itn similar to yours ( I couldn't replicate yours exactly because of the issue with the seasonal QF flights and the non-availability of the LA SCL-AKL flight ) and made the changes I suggest above and it shows as 962700 Yen. Avoiding LHR the second time will save on APD as well.