A lot of plot holes vanish once you assume that we live in an age of meaningful coincidences. However, these still bothered us.
The suppression of the manuscript is not credible. The book was published in 1993, presumably written somewhat before that, and set at still an earlier time--so possibly it was too soon to simply post a translation of the manuscript on a web page. But didn't anyone in Peru have a fax machine? Even paper manuscripts are notoriously hard to stamp out. The Soviet Union with all its totalitarian bureaucracy wasn't able to suppress manuscripts--why would Peru be able to? Somebody would have xeroxed the original and buried a few copies; the authorities would never find them all.
Cardinal Sebastian is not credible either. His position is that of a Protestant fundamentalist, not a Catholic. The rigid rejection of evolution, the deification of scripture, the denial of any subtlety or mystery in the interpretation of scripture--none of this is Catholic. (A more likely Catholic objection is that the manuscript gives no special role to either the institution of the church or its sacraments. Individual intuition unmediated by an institutional structure is something that the church has objected to for centuries.) And how did a cardinal get control of troops? The Peruvian political system doesn't work like that, and the Vatican disapproves of such relationships anyway.
Friends who have lived in Peru assure us that the descriptions of the countryside are not even close. Moreover, when you get out into the rural areas, much of the population doesn't even speak Spanish, let alone English.