For the upload and related links, there are 7 locations where links need to be modified:
1) Ribbon - Documents - New Document > Custom Action Hide
2) Ribbon - Documents - Upload Document > Custom Action Replace
3) Ribbon - Manage - View Properties > Custom List Definition (schem.xml) - Form
4) Ribbon - Manage - Edit Properties > Custom List Definition (schem.xml) - Form
5) ECB - View Properties > Custom List Definition (schem.xml) - Form
6) ECB - Edit Properties > Custom List Definition (schem.xml) - Form
7) "Add new item" >
- Custom List Definition (schem.xml) - View - XslLink
- XSL - Custom vwstyles.xsl
Steps 1 & 2:
http://msdn.microsoft.com/en-us/library/ee537543.aspx
http://msdn.microsoft.com/en-us/library/ms460194.aspx
http://msdn.microsoft.com/en-us/library/ff407619.aspx
<?xml version="1.0" encoding="utf-8"?>
<Elements xmlns="http://schemas.microsoft.com/sharepoint/">
<CustomAction Id="Ribbon.Library.Actions.ReplacementButton"
Location="CommandUI.Ribbon"
RegistrationId="101"
RegistrationType="List"
Title="Replace a Ribbon Button">
<CommandUIExtension>
<CommandUIDefinitions>
<!-- Hide OOTB Upload and New Document Buttons -->
<CommandUIDefinition Location="Ribbon.Documents.New.AddDocument" />
<CommandUIDefinition Location="Ribbon.Documents.New.NewDocument" />
<!-- APC Upload Button -->
<CommandUIDefinition
Location="Ribbon.Documents.New.Controls._children">
<Button Id="Ribbon.Documents.New.AddDocument.ReplacementButton"
Command="ReplacementButtonCommand"
Image16by16="/_layouts/apc/img/apclogo16.png"
Image32by32="/_layouts/apc/img/apclogo32.png"
LabelText="Upload Document"
Sequence="1"
TemplateAlias="o1" />
</CommandUIDefinition>
</CommandUIDefinitions>
<CommandUIHandlers>
<CommandUIHandler
Command="ReplacementButtonCommand"
CommandAction="javascript:alert('This button has been replaced.');" />
</CommandUIHandlers>
</CommandUIExtension>
</CustomAction>
</Elements>
Steps 3 - 6
<Form Type="DisplayForm" SetupPath="Layouts\MyView.aspx" Url="MyView.aspx" WebPartZoneID="Main" />
<Form Type="EditForm" SetupPath="Layouts\MyEdit.aspx" Url="MyEdit.aspx" WebPartZoneID="Main" />
Steps 7
Essentially you'll be updating an XSL file.
Custom List Template > schema.xml > views.view.xsllink > custom_vwstyles.xsl
The blog post below walks you though all of the steps:
http://byteloom.blogspot.com/2012/01/custom-upload-form-for-document-library.html
Update
It looks like the upload page property is associated with the SPWeb not the SPList object per: http://msdn.microsoft.com/en-us/library/microsoft.sharepoint.spweb.customuploadpage(v=office.14).aspx?cs-lang=csharp