Create code behind file after aspx has been created

If manual conversion is too time-intensive, and the automatic conversion isn't working, I think your only other option would be to build your own converter. You could write a simple console app which takes a directory path on the command line and processes every file in that directory. This isn't too hard - here, I'll get you started:

using System;
using System.IO;

class Program
{
    const string ScriptStartTag = "<script language=\"CS\" runat=\"server\">";
    const string ScriptEndTag = "</script>";

    static void Main(string[] args)
    {
        DirectoryInfo inPath = new DirectoryInfo(args[0]);
        DirectoryInfo outPath = new DirectoryInfo(args[0] + "\\codebehind");
        if (!outPath.Exists) inPath.CreateSubdirectory("codebehind");
        foreach (FileInfo f in inPath.GetFiles())
        {
            if (f.FullName.EndsWith(".aspx"))
            {
                //  READ SOURCE FILE
                string fileContents;
                using (TextReader tr = new StreamReader(f.FullName))
                {
                    fileContents = tr.ReadToEnd();
                }
                int scriptStart = fileContents.IndexOf(ScriptStartTag);
                int scriptEnd = fileContents.IndexOf(ScriptEndTag, scriptStart);
                string className = f.FullName.Remove(f.FullName.Length-5).Replace("\\", "_").Replace(":", "_");
                //  GENERATE NEW SCRIPT FILE
                string scriptContents = fileContents.Substring(
                    scriptStart + ScriptStartTag.Length,
                    scriptEnd-(scriptStart + ScriptStartTag.Length)-1);
                scriptContents =
                    "using System;\n\n" +
                    "public partial class " + className + " : System.Web.UI.Page\n" +
                    "{\n" +
                    "    " + scriptContents.Trim() +
                    "\n}";
                using (TextWriter tw = new StreamWriter(outPath.FullName + "\\" + f.Name + ".cs"))
                {
                    tw.Write(scriptContents);
                    tw.Flush();
                }
                //  GENERATE NEW MARKUP FILE
                fileContents = fileContents.Remove(
                    scriptStart,
                    scriptEnd - scriptStart + ScriptEndTag.Length);
                int pageTagEnd = fileContents.IndexOf("%>");
                fileContents = fileContents.Insert(PageTagEnd,
                    "AutoEventWireup=\"true\" CodeBehind=\"" + f.Name + ".cs\" Inherits=\"" + className + "\" ");
                using (TextWriter tw = new StreamWriter(outPath.FullName + "\\" + f.Name))
                {
                    tw.Write(fileContents);
                    tw.Flush();
                }
            }
        }
    }
}

30 minutes coding, 30 minutes debugging. There are some obvious bugs - like, if your code contains a closing script tag anywhere inside, then it won't get exported correctly. The results won't be pretty, but this should take care of 90% of your code, and you should be able to clean up any problem results manually. There, does that help?

There were so many changes between .NET 1.1 and .NET 3.5, that your best bet would be to create a new project and then just create new pages for each of yours, and perhaps copy and paste from the old version to the new version, so that you have all the new changes.