There's a lot you can checkout with Blend as Indy suggests. This is really good advice.
Regarding some of your specific issues these aren't necessarily glitches. I'll comment on a couple that stand out.
Extra margin - this and padding are built into the metro controls by design. Again, in blend you can dig into this by retemplating the control and changing properties of objects within the control.
The procedure for this is rclick the control, edit template, edit a copy. Then you can look at the different states and objects and change things as suits. While doing this please keep in mind the App Certification Requirements and UI Design Guidelines.
Regarding scrollbars, these are by design hidden until you start scrolling. You can control their availability with Horizontal/VerticalScrollBarVisibility on relevant controls (or on the ScrollViewer embedded in some controls - again retemplate in blend).
Combobox isn't metro themed so is going to struggle in the fitting in department, but there are posts around where people have done work on this. ListPicker is a better fit imo from the Windows Phone Toolkit released with the RTM tools.