This paper reports the findings of the second and the third year of a four year longitudinal empirical research into the modification of 'step-by-step' instructions to practical activities which require one or more steps to be designed by the students. This method had been successfully applied for a short period for 14-15 years old students. However, the first year of the current longitudinal study, investigating the approach's effectiveness (a) for younger students and (b) over a period of time, did not produce the expected results. Therefore the research model was modified at the beginning of the second year which began in September 2017 with over 800 13-14-year-old students. Each school year they spent six lessons carrying out practical activities using worksheets we provided. The participating classes were allocated to one of three groups. Group 1 was the control group. Students simply followed the step-by-step instructions. Groups 2 and 3 were experimental groups. Group 2 students followed the same instructions, but from the beginning of the second school year their worksheets explained the principles related to the experimental design of the step-by-step experiments carried out. Group 3 students followed the same instructions, but one or more steps were incomplete and students were required to design these steps, as in the first year. However, from the second year onwards Group 3 students were taught the relevant principles of the experimental design before they started planning and carrying out the experiments. The impact of the intervention on the students' experimental design skills and disciplinary content knowledge was measured by structured tests. After the second school year of the project it was clear that both types of instruction (used in case of Group 2 and Group 3) had a significant positive effect on the results of the students disciplinary content knowledge and experimental design skills. However, the development seemed to stop in the third year of the project. In the third year, a student's achievement was influenced mostly by their school ranking.