1) File a Service Request on this. Click here to do that.
2) Have you tried, per the error message, to do a manual install? If that did not work. or the documentation references the old "Classic" CodeWarrior directory layout, then file a service request on that.
3) Various settings and controls are found in different locations in Eclipse IDE versus the old Classic CodeWarrior IDE. It takes some getting used to, and I agree that certain things (such as the build settings) are buried several levels deep when compared to the Classic UI. The engineers are adding extensions to faciltate certain actions, but some of it just simply the way the Eclipse UI is laid out.
4) File a SR on that. See 1).
Please note that Help is available by pressing F1 or clicking the question mark icon. The manuals are all in electronic format and can be searched from within the Eclipse IDE. For certain operations (such as in the New Project wizard or the Debugger tabs in the Launch Configurations dialog), a help request will bring up the relevant page of the Targeting manual that explains the various setttings on that page of the wizard.