403 Forbidden in SharePoint After Deploying Website - asp.net

We have an old ASP.NET application hosted in IIS6/Win2k3. It's a document generation application that uploads the documents to SharePoint 2003. The application uses an application pool under the user sharepointservice, which is the administrator of the SharePoint site. The web application, which has been recently migrated to .net 2.0 from 1.1, uses NTLM authentication to identify our intranet users.
As the IT administrators are on holidays, I, the developer, has been given local admin rights to the Win2k3 box. The issue is, whenever I deploy the website, though the documents are uploaded appropriately to the SharePoint site via the application, the users are not able to download them. The error is
HTTP Error 403 - Forbidden: Access is denied
I know the IT guys use a service account, not their domain user accounts.
I have already tried to modify the permissions in IIS for that website. I even put Everyone and <Domain>\Users to have read access to all of those folders, to no avail. I've scoured the net, there are no definitive answers. Am I missing something else?

I hate answering my own question, but this did it for me:
The application pools for the SharePoint site were modified from the default. So I reset them, including the AppPools for _layouts, _vti_bin, and _wpresources. Their AppPools are now the default, and are the same.
This link gave me the lead.

You are probably being prompted by permissions for the file system. Check the directories where IO is happening and make sure the user sharepointservice is using in the app pool has read/write permissions.

I just had this problem and solved it after following these instructions:
http://support.microsoft.com/kb/2543306
It seems the webapplication took so long that it hadn't created everything correctly when the IIS timed out. So I was receiving strange errors like yours.

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Then you need to give permissions to the account in the app pool identity the names will be the same or at least be very similar to what you saw in IIS:
So using my examples above I will have to give permissions to Local Service or Network Service to read/write my app_data folder.

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Thanks.
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then publish your site to *.aspx file and *.dll file. to see if there is any errors.
So I found the issue. What I didn't know is that by default, IIS 6 does not turn on support of active server pages and .NET pages in Web Service Extensions. Once I had turned this on the site began to work just fine.

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