To get the touch position start with PreToolManagerListener.onSingleTapConfirmed method in ToolManager.java file. Once you have the touch position, which will be in screen coordinates, you would call PDFViewCtrl.convScreenPtToPagePt To get the coordinates in the particular PDF page. From there you can match up the page coordinates with your map marker.
PDFViewCtrl.convScreenPtToPagePt will handle all page transformations, including layout, zoom, position, rotation, etc.
onScrollChanged and onScale are not currently "exposed". However, as we do provide the source code for customization, you could expose these by following how the same pattern as onMove/onScaleBegin are done.