From my understanding of your question that you don't need a web based program but really need a PDF Editing tool. I am assuming you need to edit the PDF and make some changes but still be compatible with your application as you cannot change the application.
Foxit Software has a new product called Foxit Phantom that allows you to create and edit PDF form fields. It is a direct competitor to the Adobe product, is currently on special and only costs $99USD. You can download it as a 30day free trial to see if it meets your needs.
http://www.foxitsoftware.com/pdf/phantom/
If you just want to change an address or company logo then Foxit Phantom can do this easily and this would be the quickest approach with the least amout of changes.
You can design the form layout in any graphic design program and save or print to PDF. Phantom comes with a PDF printer driver. You may be able to cut the form fields from the old form with Phantom and paste them onto your new PDF and then just move them around to fit.
Your biggest problem will be your own application if you have to add new data fields. There are various ways to get data from a PDF. It would help to know if this "application" is an in-house application or a 3rd party application and the extent of the changes you want to make. Getting a look at the PDF would probably help answer some of my questions.