Easy. For starters, there's a bus (don't take it) from Venuezuela via Lima and Santiago to Buenos Aires that I was told about while there, takes a week. But gives you an idea of the max time you might spend on buses, given you're doing a bit of tracking around.
Lima to Arequipa and then Cusco can be done in 1-4 days depending on what stops you want to do. I recommend a side trip to Colca Canyon near Arequipa, go find the Condors.
Inca Trail and Machu Picchu are obviously done together, you could allow a week for acclimatisation and the trail, including some time in Cusco.
8 hours by bus to Lake Titicaca (Puno).
You don't need more than a day or two at max here. Most travellers just don't like it that much, and some feel the reed islands are a scam, but if you're like me and dreamed of seeing the lake, you can and will still enjoy it.
5 hours by bus to La Paz. 2-3 days here - things like the Death Road, exploring the city and more.
Overnight bus to Uyuni, and then a salt flats tour. Worth noting that the 'best' option is to carry on through to San Pedro de Atacama in Chile, but some do go in a sort of loop back to Tupiza, from memory.
If you did go to San Pedro, it's then 10 hours by bus to Salta in Argentina and another 20 to Buenos Aires. Heck, you could even go down to Santiago and Mendoza (wine country!!!) and then across to Buenos Aires. See how your time is going and go with the flow.
I've not been to Bonito and the falls, although I'd ask why not Iguazu Falls?
However, the main thing - don't overplan it. Give yourself 6 weeks from Lima to Buenos Aires, and pick the things that are absolute musts. Then let other travellers fill in the gaps with suggestions. You may find yourself in Nazca, seeing the Nazca Lines, going to the jungle in Bolivia, wine country in Argentina, or even down the coast from Buenos Aires (20 hours) to the wildlife area around Puerto Madryn (whales!!).
I spent 4 months tracking around several of these countries, but a friend I traelled with for a bit went from Santiago and Mendoza, up to Iquique, across to La Paz, Lake Titicaca, Cusco + Machu Picchu (train not trail though), Arequipa and Colca Canyon, Nazca and Lima in 3 weeks, without rushing. Yes it's a lot of bussing, but you get used to it, and some of the buses in Peru, Chile and Argentina are surprisingly luxurious for a few extra dollars (think beds!). Look for full-cama/cama-suite buses.
I didn't finish all my posts on South America, but my blog has quite a few posts on some of the places you are talking about, which may be of interest for timeframes - I tend to describe the transportation quite a bit too.