Okay, so you have someone who will fill out the forms for each response? You say these come in via PDF?
It sounds as if the form does NOT have to be a browser form, is that correct?
If it doesn't have to be a browser form, you can either base your form off a database (I'd suggest SQL rather than Access -- there is a free SKU if cost is an issue) or you can buy or build a web service (I'd be remiss if I didn't point out we sell an excellent one here.) Building off a database means the DB has to be designed before you create your form, and it creates a tight coupling between the form and the DB that can be challenging to work with, however, if you do that, InfoPath will be able to use its built in Submit capabilities. I'm having a bit of trouble envisioning what the DB design would need to be like for this -- I've gotten spoiled with submitting to web services, I'm afraid.
You can use conditional formatting or optional sections to decide what to show or hide in your survey.