As Okieboater mentioned, the Aulback series are "the" guidebooks to have. Although likely not enough time, I would highly recommend reading Keith Bowden's book Tecate Journals for local color. For my trip, I exchanged several emails with him which were quite helpful. He's floated (at least the lower canyon) the river more than anyone else I'm aware of. I also got a lot of information through the BigBendChat.com site which has a river forum. The NPS also has a free river guide that was better than expected, although the ratings they assigned to the few rapids were ludicrious.
Santa Elena worldclass. Mariscal not quite so but still very good. Although it was not a vehicle from our group, one shuttle vehicle left at Solis had a window smashed with the car apparently being rifled through.
The last float I did was in 2007 and the NPS/Border Patrol/Federales was still sorting through the new reality. At that time, officially you were not to land on the Mexico side, but everyone did. Fern Canyon was a must see for us and it's across the border. My understanding is that the situation is much more restrictive now. I would definitely talk to Far Flung about this. As a permitted outfitter, their official stance would mirror Homeland Security, but the under-the-counter advice might be different. Be aware that a possible gotcha is that if you do get caught on the wrong side, you can only re-enter the US through an approved border crossing. That could well be hours and hundreds of miles from where you get caught. Have used Far Flung and had no problems.
Others have discussed flow/canoes vs kayaks/etc so won't dwell there and I've only done monsoon floats anyway.
The whole crime/drugs/cartel/border patrol/federale/wetback (you could well see someone with water dripping off theirs) issue is a sensitive one for lots of people. The most common advice is to ignore it all and play the tourist role. That is what I've always done and it's worked well. Keith Bowden also told me about where 3 trips in a row he found a headless body in the river. We went through a border patrol checkpoint but it was well away from BBNP and we apparently did not trigger any obvious flags as we were waved through without stopping. On the last trip had heard an unverified rumor that the DEA crossed the river at night in rafts to cut down a pot plantation that the Mexican Army had growing. This was in Colorado Canyon across from Big Bend State Park. I kept thinking about that when we did a day hike up Arroyo El-Rinco on the Mexican side in that area.
We've never had an issue, and it's a great (though not white-water) trip, but it's also not the San Juan nor a Boundary Waters trip.