We had the same issue, and we solved it like this:
One of the things you have to solve is the duplicated global.asax files.
1 - Define one of your projects to be the mandatory. Let's say your mvc project.
2 - On the webforms project, create a reference to your mvc project dll.
3 - Remove the code behind in webforms app and change your global.asax file in your webforms project:
<%@ Application Codebehind="Global.asax.cs" Inherits="Your global class full name" Language="C#" %>
Inherits must have the fullname (namespace+class) from your mvc global.asax class. For instance: Company.App.Application
4 - Make sure you are referencing the same versions of assemblies that are common to the two projects.
5 - Who works with the mvc project must have access to the code of webforms project and vice-versa.
6 - Make sure both projects are referencing the same web.config file.
7 - Then you can publish first project webforms and later project mvc.