One free pin. Need to display output for the user?
Seems you have I²C on the board you could possibly use an I²C LCD backpack, like from breakouts if you already have an LCD, this means you can have the RTC and display on the I²C bus and probably more things.

Another option seems you mentioned LEDs, you could still use the I²C bus and use an I/O expander and hook LEDs up to that and address them over the I²C. You can use a PCF8575(16 I/O), as there are Arduino libraries. There are breakouts for it. Or you could make your own from another AVR, like one from the ATTiny line, seems there is 5 LEDs.

A I²C bus example:

(source: ermicro.com)  

Seems you want to use the PWM, you can use a dot/bar driver IC, such as the LM3914 it takes an analog value and shows it as a point on the strip of LEDs, example below:


The IC can also work down to 3V. 

What you will need to do is add a low pass filter to convert the PWM to a smooth analog value. You will add this in place of the input circuitry(D1 &amp; C1) there:



If there is any confusion on the LM3914, there are quite a few tutorials on google.