How have you been trying to focus with your manual lenses? Please explain your methods, then I can help give tips. Some people suggest using Catch in Focus (I don't know how to get this setting, if someone else can jump in...) to do manual focus shots - it let's the camera activate the shutter while you rotate the focus ring the moment it feels it is in focus.
For the kit lens, you can check whether or not your camera is acting up in focus or not. Try testing the focus. Set the camera out of focus, then aim at your well lit subject and focus and shoot. Aim for something that you can determine if the camera focusing too much to the front or back, example:
If the camera aim's too much to the front or back, you can see it on the girder. Let us know your results.
The shot of the orange is quite nice. The shot of the leaf shows motion blur and out of focus (the exif shows 1/10s shutter, so definitely motion blur). The shot of the bird is very very nice. So my suggestion is to practice in bright lighting (daylight) as those are helping you get good results. Use Av mode with your kit lens and let the camera choose the shutter. Try to keep your aperture at F4-8 depending on the brightness outside.
One thing about autofocusing - your kit lens is F5.6 on the 40-55mm end, and that is very dark for the camera. Indoors, that would make it tough to autofocus - when you get used to the camera you should start thinking about getting a better lens for indoor use.