I am pretty sure that what you need to do for all of the content to fit properly in PDF is to use the "Page View" setting/mode on the Design tab (default view is "Web View" for web forms) and edit the content in that view to "fit". The "Page View" view mode is to design/tweak the form to work in PDF, the changes made in "Web View" are still there including all features not supported in a PDF, but any Page Breaks added in either view are unique to that view, if you add a Page Break in Web View you will not see that in the PDF or Page View, if you add a Page Break in Page View it is only used in the PDF.
If you were to have used the "Save Submission Enabled PDF" button on the Distribute tab you would have seen an error that the content does not fit and it would have taken you into "Page View" on the Design tab where it would show you the content that would be cropped in a PDF. We'll address the issue that this error does not come up when saving the response as a PDF form.
The view drop down selector is in the bottom right corner in the Design tab:
There are a few things you can do in Page View to get the content to work in PDF but not change the HTML/web form too much. You can of course add page breaks, and you can break up large form fields, but you can also simply change the font size to get things to fit sometimes, or go into "File" - "Form Setup" and change the page size which will only affect the PDF and not the web form, a larger page will fit more content.
Hopefully this helps but let me know if this was not the solution to your form.