Yeah I know TLH deals with the emergence of the villains and how they take over from organized crime. Year Four would be more about the transition from that phase to the full-blown comic-book craziness of the Silver Age. Thematically speaking, its about the time between the origin of Robin and the Adam West TV show/classic Batman cartoons.
As far as Year Two goes...yes, I know the actual story isn't canon anymore, but hell, maybe even parts of Year One didn't happen the same way in whatever is 'current' continuity. I'd take a broad strokes approach to the whole thing, wherein some aspects of Year Two did happen, mainly the conflict with the Reaper.
I'd actually open Year Four with a page with three panels - Batman breaking into the mayor's mansion from Year One, Batman fighting the Reaper from Year Two, and Batman bringing Dick into the Batcave from Year Three. And then Year Four begins.