I guess this thread is a bit old, but I thought I'd chime in with what I implemented in RFCW and the beta of TTW.
I concur with those who like the idea of the LW being recruited to join the Mojave Express. I also took into account that the Wasteland Survival Guide had to be written before getting the quest. While I completely agree that once the LW sets in motion the events at the Purifier after rescuing Dad, it didn't make much sense to allow the LW to travel across the country to become a mailman. Of course, it also doesn't make much sense to me either that he would stop and help slaves in Pittsburgh, pay the Outcasts a visit and do a VR sim, or take a vacation to Point Lookout for mutant fruit, and the game doesn't block those off, so I just sorta didn't implement any sort of "block" to prevent my quest from being available at various stages of the main quest.
What I did was spawn 3 NPCs at the gate of Megaton that would appear at the conclusion of the Wasteland Survival Guide quest. 2 of the NPCs were just guards for a member of the Mojave Express who have made the perilous journey eastward after accepting a contract from a cowboy faced robot to retrieve a platinum poker that was mistakenly delivered to the RobCo factory in the DC area. The LW then has the option to go to the RobCo factory and find the chip. Upon finding it, the LW exits the building and gets an invitation to travel with them back west, forget the troubles of the highly irradiated and dangerous Capital Wasteland, and work as a courier for the Mojave Express.
When the LW accepts the offer, the Mojave Express rep tells him that it's going to be a long journey, but you'll be burstin' with caps when we get there. From there, I just faded to white and showed the "Three Years Later" bik, and from there, I just started the intro quest at Doc Mitchells, complete with NV intro bik and all. I disabled the Vigor Tester, because it seemed pointless to reallocate SPECIAL points. I went ahead and had the LW/Courier go through the psyche tests, I figured it might be neat to be able to re-select tag skills and traits... especially if you are really RPing, you might want to give your guy some different traits since he's been shot in the head.
From there, you just play the NV side to your hearts content, and when you're ready to venture back east, head over with your preferred method of travel. I confess, I was skeptical of the train method (and still am from a lore perspective,) but the work that has been done on the train is professional quality, comprehensive, and when you use it, it doesn't feel like breaking lore at all. So yeah, I say keep it in. If it remains a problem for some, might I suggest you make it a plug in like the bobblehead perk plug in?
I would also add that I love your ideas for the updated Vertibird travel method. It did seem a shame to not use those videos that the author of the original mod made, and the concept of flying cross-country in a Vertibird does seem the most lore friendly of all.