That's a lot of questions in one post! Here are some ideas.
First the pear tress. Thin out the fruit each year so that they are about 10cm apart. This will produce fewer but better fruit. It will also avoid damage to the branches.
I would ignore the green flaky stuff, it sounds like lichen. If it is though, it's an indication that conditions are too damp, so think about how that can be improved.
As for the apple trees, many varieties produce lots of fruitone year and then very little the next. The general rule for pruning apple trees is to allow about four main branches and prune to a wine goblet shape. Leave the centre relativley free of branches to allow air circulation.