The best way to run the program is exactly as it is written. Having said that, there are a few changes that are recognised as being acceptable, some that may become necessary, and some that people are just going to do no matter what you try to tell them.
Changing the calf raise rep rangeEdit
The reason the rep range is the same (8-12) for all exercises is to keep the program simple. It also happens to be an optimal rep range for most people, for nearly all the exercises. The most likely exception is the calf raises. Calves have a very small range of motion and 8-12 reps doesn't force them to do much work. Changing the rep range to 12-16 can hit them a lot more effectively.
This is a widely recommended variation to the program.
Increasing weights by more than 10%Edit
After the first cycle or two, it is highly unlikely you will be able to do this. However, it is not unusual to be able to raise by 15 or even 20% for some exercises at the end of cycles 1 and 2, particularly for users who started light in order to focus on good form.
You should be aware that unless your starting weights were way off, there is not a lot of point to doing this. You will very probably be at about the same point after a few cycles whether you stick to 10% or not.
Increasing weights by less than 10%Edit
A few cycles in, even 10% may not be achievable. Otherwise, we'd all be benching 3 tons after a couple of years. At this point, you will need to consider how to raise weights by a smaller amount - fortunately, you'll have enough experience by then to deal with it sensibly. The simplest way to do this is to change the math - just raise by 7.5% or 5% instead! Other options might include extending the length of the cycle, for example by using a 7-12 rep range over 6 weeks.