So I started digging. First thing we found is that Web Access can get cranky if Custom Work item Controls are missing. Visual Studio will happily render a TextBox or DropdownBox so that you get some working UI, Web Access behaves slightly different; it just hides the whole control from the form. So if you're using any custom controls, make sure that they're installed on both the Web Access server and inside the version of Visual Studio you're using to change the process template. They should be listed and enabled on the Admin page:
And then the second thing we ran into, is that many of our old work item definitions used to have more than one
A thing to look out for when using the Power tools is that again it doesn't show you everything. When you open a WIT that has multiple layouts, the Power Tools designer will only show you the *first* one. It doesn't even tell you that there are others.
Just a few lessons learned :S.