The first and most important lore deviation I made is in Vault 112: I locked the entryway door and installed a control console next to it. You won't open it without the Platinum Chip, meaning that you won't be able to start Waters of Life until at *least* you deal with Benny. (Trust me, it'll make sense, even though those specific story elements have not yet implemented in this early mod release.)
The second major deviation I made from TTW proper is changing the train time gap from nine years to three. In this rethinking, the Lone Wanderer hit dead ends while looking for Dad and sort of had to make a life as an adventurer for a longer period of time than in canon. Months go by, and the LW finds the train at some point in early-mid 2278 rather than in late 2277. A bit over three years pass from that day, and the NV portion of the story picks up in October 2281 without much deviation at this time.
There are now a handful of new narrative additions to the DC wasteland, mainly in the form of terminal entries and holotapes. There's the start of a backstory involving the Brotherhood's use of civilian contractors in 2274-2276, and a small group of said civvies who were following the trail of highly sensitive prewar tech. There's also some new stuff telling a brief story about a Capitol Post reporter covering the Union train story.
I plan to add more material in both DC and NV, points connecting House, Robco, Repconn, Vault Tec and possibly a bit about prewar Enclave.