About the difficulty of being sure which object the cursor is on, this is a problem with whole measure rests when other notes are in the same bar (which of course is never intended).
It helps in this circumstance to watch the status bar at the bottom of the display as you move left and right with the arrow keys. You are told the number of the object in the bar that you are on, and what type of object it is (and whether you are in the appending position after the last object in the bar). Moving back and forwards with arrow keys allows you to be sure which object is the current object.
For deleting you then use Del,Del or move right and use backspace.

An alternative is to drag downwards so as to mark the current object, the whole measure rest is a big block while the note next to it is much slimmer just over the note itself. Then you can use Ctrl-x to cut the object.
Fixing the Merge to cope with whole measure rests is on the back-burner at present.