Digitally signing a PDF document without using a third-party component entails a great deal of work and is generally best avoided.
Components do all the hard work for you, so you don't have to. You should find there are some excellent free PDF components available that will suit your needs.
The following example written in C# shows how simple it is to digitally sign a PDF document using ABCpdf:
Doc theDoc = new Doc();
theDoc.Read(Server.MapPath("../Rez/Authorization.pdf"));
Signature theSig = (Signature)theDoc.Form["Signature"];
theSig.Location = "Washington";
theSig.Reason = "Schedule Agreed";
theSig.Sign(Server.MapPath("../Rez/JohnSmith.pfx"), "111111");
theDoc.Save(Server.MapPath("Signed.pdf"));
Source: ABCpdf documentation - Sign method