Here's one way with sed:

sed -E '/with_ajax_wait/,/end/{       # if line is in this range
H                                     # append to hold space
/end/!d                               # if it doesn't match end, delete it
//{                                   # if it matches
s/.*//                                # empty the pattern space
x                                     # exchange pattern space w. hold space
s/^(\n)( *)/\2it "waits" do\1\2/      # add first line + initial spacing
s/\n/&  /g                            # re-indent all other lines
G                                     # append hold space to pattern space
s/^(( *).*)/\1\2do/                   # add the closing 'do' + initial spacing
}
}
' infile

so with an input like:

with_ajax_wait
  expect(css_coverage_type_everquote).to be_visible
end
  find(css_policy_form_stage3).click
  with_ajax_wait
    expect(css_coverage_type_everquote).to be_visible
  end
  something here
    with_ajax_wait
      expect(css_coverage_type_everquote).to be_visible
        got some more stuff here to do
          process it
        done
    end
  end

the output is:

it "waits" do
  with_ajax_wait
    expect(css_coverage_type_everquote).to be_visible
  end
do
  find(css_policy_form_stage3).click
  it "waits" do
    with_ajax_wait
      expect(css_coverage_type_everquote).to be_visible
    end
  do
  something here
    it "waits" do
      with_ajax_wait
        expect(css_coverage_type_everquote).to be_visible
          got some more stuff here to do
            process it
          done
      end
    do
  end

It should work with blocks of more than three lines provided your with_ajax_wait blocks always ends with end.
Replace the closing do with end if needed as your example is confusing... (you used end for the first block and do for the second) e.g. this time using BRE and [[:blank:]] instead of (space):

sed '/with_ajax_wait/,/end/{
/with_ajax_wait/{
G
s/\([[:blank:]]*\)\(with_ajax_wait\)\(\n\)/\1it "waits" do\3  \1\2/
p
d
}
//!{
/end/!{
s/^/  /
}
/end/{
G
s/\([[:blank:]]*\)\(end\)\(\n\)/  \1\2\3\1end/
}
}
}
' infile

This one is processing each line in that range separately, the first and the last ones in the range are re-indented and wrappers are added, the rest of the lines are just re-indented.