You may restrict your experiments to a subset of the dataset IF Weka cannot handle your whole dataset (this is unlikely though).
A main part of this project is the PREPROCESSING of your dataset. You must apply relevant concept hierarchies and generalizations (e.g. using the results of previous mining tasks) to your dataset before clustering it. Your report should contained a detailed description of the preprocessing of your dataset and justifications of the steps you followed. If Weka does not provide the functionality you need to preprocess your data as you need to obtain useful patterns, preprocess the data yourself either by writing the necessary filters (you can incorporate them in Weka if you wish).
Your report should contain the following sections with the corresponding discussions:
Provide a detail description of the preprocessing of your data. Justify the preprocessing you apply and why the resulting data is the appropriate one for mining clusters from it.