My feeling about J/S: he's in Paraguay, the deception of the author wouldn't go as far as this.
But don't other readers feel like me that Toomawoomba was the apex for the Scar? I think that he could manage building/ planting the bomb, which shows he had some leadership/ engineering skills, but since he's scared the planet s***less, it's going down the hill, because his HR management are quite poor, beyond having people they'll be highly paid and then killing them.
I don't think he can manage a coup in Paraguay. The dynamics in South America are not the same than they used to be, and Paraguay has been democratic since 1992. Hence, since this is supposed to happen in 2010, he has to deal with people who've known democracy for almost two decades. He would need to have the land owners and the big company owners, plus the police AND the military if he wanted to succeed and enjoy a few years of peace. He'd have been better off buying an island in the Caribbeans (or in the Pacific), with one bomb cleverly hidden.
I think the wiping out of Instinct was poorly planned. It should have been in the blueprint of his general scheme, and handled way before, and he should have had a B-plan for the last bomb, not relying on the same "band cover-up" stuff for all of them. Plus relying on someone like Dimitri is kind of stupid, since he's quite unreliable. (The fear of height, the killer's instinct...)
I'd bet CJ could open some workshops in some remote location in the Arizona desert (there seems to be mine shafts galore over there, perfect for this kind of events), World Domination 101: Soft and Hard Skills to Become a Faultless Criminal Mastermind