The Border Route was part of Andrew Skurka's "Ultralight in the Nation's Icebox" trek last January. (listen to podcasts here at BPL) IIRC, he reported a single day on the Border Route where he encountered a large number of deadfalls (200??)
The current conditions page at www.shta.org starts out with "Unless you plan your trip very carefully", implying that it'll be possible to plan a successful hike. I've section hiked the entire SHT, many sections multiple times and from what I recall plus the detailed report from the trail assn I think it'd be possible to hike the trail using the reliable water sources and "camel techniques" plus about half a dozen water caches.
Also, the area received a little rain the last couple days and the forecast for the next week includes rain as a possibility on about half the days ... so it bears watching.