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It is recommended that you not set any security settings on the PDF version of your thesis.
PDF files larger than 100MB may result in slower than optimal access.
If your PDF file is large, you may want to consider the format and resolution of your images (modify the format and resolution before inserting images into your thesis. A good format to consider is .jpeg).
You may also want to consider submitting some images separately. See procedures for submitting an enhanced thesis.
Other suggestions regarding reducing the size of your PDF file can be found on the Adobe website.
Save your thesis PDF file as Lastname_Firstname.pdf (replacing 'Lastname' with your last name and replacing 'Firstname' with your first name (without any diacritics)).
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You may use another 3rd party product; such a product for Windows is PDF Creator. PDF Creator is Open Source, so there is no charge. It can be downloaded from the SourceForge project page. It actually uses GhostScript in the PDF conversion process. However, unlike GhostScript which processes a PostScript file, PDF Creator installs itself as a printer on your system. When you want to create a PDF file from any application, you choose your application's Print command, and PDF Creator will create the PDF file.
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This procedure is available in the Adobe Acrobat XI Quick start guide (PDF).