|I FINISHED!!!!! It's worth it.|
CONTAINS SPOILERS FOR CRYPTONOMICON AND THE BAROQUE CYCLE
The Baroque Cycle explains almost everything in Cryptonomicon, such as the contents of the NIZ-ARCH (LeibNIZ-ARCHive) crate the Shaftoes fish up from the wreck of the super U-Boat. Also, the ancestors of many supporting characters get their stories told--Gabriel Goto, forebear of Goto Dengo, Moseh de La Cruz-->Avi, The Gold Comstock-->Attorney General Comstock, etc.
Princess Wilhelmina Caroline, before she became George II's Queen Caroline, *did* try to reconcile Leibniz and Newton. I knew Newton hadn't croaked at the Trial of the Pyx because I'd sneaked a look at his bio online.
Jack Shaftoe *does* say "I didn't expect the Spanish Inquisition" when Father de Gex turns up. There are lots of Easter eggs sprinkled in the book.
The state of clockwork c. 1700 was reflected pretty accurately. Half the time bombs go off at the wrong times. They're only useful for setting off explosions when you're far away and have an alibi.
I'm staying with one of my original guesses about Enoch Root--that he stumbled on the Immortality Juice and quickly figured out (as does Leibnitz at the end) that, while it keeps you alive and healthy, it's no smart drug. He also found a purpose, which was helping out in ways that would, he hoped, later form the basis for myths that promote intelligence and some kind of wisdom. Neither is especially prized by the general population or its leaders. If he's really old, he could be Enki or a priest of Athena (judging by his prison lecture in "Cryptonomicon"). He might have picked Enoch as a name because of the Biblical reference, though there were mature civilizations around then capable of alchemy. There's never really a physical description of him, except he's Caucasian and has red hair, which is probably real. Didn't Gilgamesh or Enki have red hair?
He also honed his knack for staying alive. The entertaining bits of history are dangerous, but even non-history can kill you off before your allotted time. Root also knows when to make an exit. Dying on the operating table in WWII was a convenient fiction. There's an Enoch Root-shaped figure ducking out the back immediately after the doctor signs his death certificate.