You are hoping to do three things:
- Gather the data using an ordinary web application.
- Insert that data into a PDF form that has been created to match a paper form.
- Serialize and transmit the resulting PDF to somebody by email.
You have done the first of these things. The third of them is quite simple, once you have the file you want to send.
The second one is difficult. You have two choices.
Write a program in your favorite programming language to generate a pdf that replicates your paper form. This is an incredibly tedious task, but you can do it, line by line and text string by text string. Look up the PDF api inside php. http://php.net/manual/en/book.pdf.php
Use Adobe Acrobat to create the form. You can scan the paper form and then insert form fields in the appropriate places. You can test the form, edit it, and make sure it is correct using Acrobat. (Notice that an Acrobat form is not just a PDF document; it has fillable form fields). Then, once you have a good form, you can write some software to fill in the fields of that form and save the result.
The second process will give you a professional looking result, but you'll have to spend money on a full copy of Acrobat (or some other forms-capable PDF tool).
So, once you have a nice pdf form, with named form fields, to use as a template, the steps are: