I did try to do the whole thing over the phone but the issue was they were adamant that some of the flights weren't available - Bangalore to Sydney for example. Not sure why the differenceVery nice itinerary, well done. I had to look up Cabo.
Your transit in India is likely to be much more comfortable if you get a visa and go landside - there are horror stories of transit pax having to wait on hard seats in a holding pen until an airline rep rescues them 2 hours before their onward flight. Much more comfortable to wait out the transit time in a nearby hotel.
Just for others' reference, you could have avoided the 5,000 point change fee by booking the entire itinerary over the phone rather than doing some flights online. But it is a small extra price to pay for getting an interesting itinerary.

I've been looking at the Bangalore transit and think the 080 hotel might be go - you can get and airside room for 12 hours for ~$130 which sounds perfect.