You know when you ask 100 photographers for an opinion, you'll get 100 different ones. Right?
I thought the first one was fine. I like the bars because it personalizes the image more because you KNOW it's in your backyard rather than some arbitrary image you took somewhere else. I think it's also more 'candid' looking too with the bars. But it depends on what you are going for. A personalized image or an image of deer.
Yes, focus looks to be on the bushes rather than the animals. Lightroom can help you fix that a bit. I've only used LR4 and above so can't tell you about LR3. I saw a special for snagging LR5 for about $70. Totally worth it. But to get it right the first time? AF isn't always going to nail it. You'll have to figure out which AF point selection will work for you. And that will change depending on what you're photographing.
I like the coloring you did in the second picture. Very tasteful. Often people go overboard with that.
The general rule is that to minimize blur for hand-holding a camera, your shutter speed needs to be 2x focal length. So if you are using a 100mm lens, you should be shooting at 1/200 sec at least for digital. In the film days, it used to be focal length = shutter speed. Even shooting at 300mm, 1/1000 should be plenty.
There are definitely wild life photographers that use tripods. Maybe not on the back of a jeep. But if they are watching animals from a distance: definitely. You see it all the time from those types of photographers. They'll be camouflaged out in the bush for hours waiting for that particular animal to come walking by or come out of their shelter. You bet your ass they'll have their camera on a tripod.