I am a little curious why fast auto focusing is important for the two types of photography you listed: landscape and portrait photography. I am a landscape photographer myself, and I find that I usually (90% of the time at least) manually focus my shots with all of my lenses. I would also figure that manually focusing portraits would be ideal, as autofocus algorithms are generally somewhat "fuzzy", and don't always lock on to the most ideal thing. In portraits, you really want the eyes to be in perfect focus, but you are not guaranteed to get that with autofocus, even with the best AF lenses. I guess if you are looking more for a "shoot from the hip" or fast studio shooting, AF would be a necessity.
There are plenty of great cameras out there on the market these days for under $1000, and you can usually get at least one, if not two, kit lenses with a decent DSLR camera body for that price. I am a Canon user myself, however Nikon, Sony, and others also make great cameras in the $1000-$1500 price range. Best bet, you could probably go with any entry or mid-range camera body (body only), and grab a fast 50mm lens (i.e. an f/1.4) for around $1600. You might even want to look into getting a great manual focus lens. Zeiss makes some superb fast 50mm portrait lenses with nice soft focus. Canon makes some manual focus tilt/shift lenses at 17mm (ultra wide, can't use filters), 24mm, 45mm, and 90mm that can do wonders for landscape photography, and bring a dynamic focal plane to your portrait photography (the effect can be wonderful.)
If you insist on top of the line autofocus, you can get that too, although the best AF will cost. For landscapes, again, being a landscape photographer myself, I highly recommend going with manual focus. I have quite a few Canon L-series lenses with excellent AF, however when it comes to landscapes, your depth of field is often huge, and AF can only do so much. Manually tuning focus with the live view feature is the only way to get focus exactly how you want it with landscape photography. For portraits, there are usually great 85mm and 135mm AF lenses that will do the job, however you might need to spend a bit more on the lenses to get exactly what you want.
Regarding camera bodies, they are "a dime a dozen". A decent body today will be bottom rung in a year or so, and you may find yourself regularly upgrading camera bodies every couple years. Lenses, on the other hand, can last a lifetime. If you want to spend your money wisely, I would say there is more long-term value in lenses than in camera bodies...provided you stick with a single brand consistently. Quality glass can and will do wonders for your work. A new camera body every so often will provide you with a little more control and certainly more resolution.
If you really want to nail those shots that need good AF, then putting some money into a decent camera body might be worth it. An example of a great high-performing AF body would be the Canon 7D. This camera has an amazing, cutting-edge AF system with adaptive capabilities and superb low-light, high ISO performance. This camera also has a more advanced, color metering system that should help you nail perfect color rendition without much effort. Combined with good glass, a Canon 7D will really help you nail those spur-of-the-moment candid portrait shots that you are looking for. The price point is certainly higher here...the camera body alone weighs in at around $1600 or so, and you would still need to get some decent glass, like the Canon 50mm f/1.4 lens and maybe the 85mm L-series lens (one of the best portrait lenses available from Canon, if not the best.) You might be looking at about $2000 for a decent Canon 7D setup, but the AF performance of a pro-grade body like this is nothing less than astonishing.