So, I've virtually planned this brief South American taster.
Originally, was set to go to Hawaii for the fortnight, though something got mentioned about machu picchu and bam suddenly that was an options.

Essentially going to do the first bit by tour, to hopefully avoid any early hiccups.
Arrive on the Sunday and start tour that day hopefully. They say arrive anytime and time difference means we would arrive around 6pm. Day 1 is simply arrive.

Day 2, fly to the amazon as part of G adventures tour, formerly GAP.
Days 3 is amazon
Day 4 is flying to Cuzco and city tour
Day 5 is day trip to ruins around Cuzco
Day 6 is first day of inca trek,
Day 7 is day 2
Day 8 is day 3
Day 9 is macchi picchu and return to Cuzco
Day 10 is checkout and finish tour. Hoping to fly to iaguzo falls after a flight to Lima and then to iaguzu, apparently arriving around 6-7pm.
Day 11. Iaguzu falls with potential afternoon flight to rio.
Day 12 fly to rio or be in rio
Day 13 be in rio
Day 14 rio and an evening flight en route home.

Very busy jam packed 2 weeks.

How reliable is air transport timing wise? Do they cancel flights frequently? Or is it hit and miss.

And how much time to get over jet lag roughly?

I'm still a bit 50:50 on a relatively expensive jam packed adventure or a nice relaxing trip to Hawaii. My time in Hawaii would more than likely be spent at the beach or climbing their mountains/volcanoes.