One tip is that if you have a problem with bugs or fungus, do NOT compost those plants in the same compost you intend to use the following year. Start a second pile, being sure that it gets good and hot as it decomposes (160 degrees or more, if I remember) to kill all the eggs.
If your problem is with contaminated/infested soil, plant a different crop there next year and grow the original plants someplace else.