If going through Bolivia twice, I suggest that you one way via the higlands – La paz – Oruro – Uyuni (Salar etc) – (Would be great to go to via Tarija if you have the time) – Potosi – Sucre – Santa Cruz – Corumba – Brazil
Then on the way back enter via San Matias – San Ignacio doe Valesco - Concepcion (visti Noel Kempff, if you have the time) –San Javier –Ascension – Trinidad – San Ignacio de Moxos – San Borja – Rurrenabaque (lots of jungle/pumpa tours from there) – Caranavi – Coroico – La Paz.
From La Paz you can do short trips to Sorota, Tiwanaku or Copacabana (depends where you crossed the border from/to Peru – you can either visit Tiwanaku on the way there or out and so with Copacabana).
Just be aware that the best time to visit Bolivia is May – September (actually July-August) . Lowlands are flooded during summer (November – March) and roads often impassable due to landslides (mountains) and flood (lowlands). Also you seem much more wildlife in the pampas during dry season (July – August). Salar is also best during that time as it is usually sunny, but very cold. Only disadvantage is that there might be lots of smoke in the lowlands due to burning of the jungle/fields which is done during the dry season
Have fun
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