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The jumper block won't work this way. In your software you can define the AVR input pins as Hi-Z or with pull-ups. When you define them Hi-Z, they will be floating when no jumper is present, and you'll get random readings. When you define them with internal pull-up, your input will always read '1', regardless if you have a jumper or not.
You should get rid of the resistors and tie pins 2,4 and 6 to ground. Define the input pins with pull-up. No jumper always reads '1', jumper present reads '0'.
You probably also want to re-arrange the pins a bit. If you leave the jumper block on the MOSI/MISO lines, you will have to take all jumpers off before attempting in-circuit software updates.
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