Note: with your MSI you have to do two steps:
1) Run it as MSI to install artifcacts on Window and in GAC
2) Import it into the Biztalk Admin Console so populate the Biztalk Mgmt Database
Here’s a big trick I learned the hard way. You can attach .NET C# .DLLs as a resource to your application, but when you re-export, it doesn’t grab the latest .DLLs from the disk (i.e. somewhere it is keeping the old copies). You have to drop the resource, and re-add it to get the latest .DLL. So if you change a non-Biztalk .DLL resource, remember this step before you migrate again.