I can't help with the pop up but, in place of that, I suggest that you use a bell sound.
You should have a wav sound file for this and you could use a bell sound like org-pomodoro's.
From C-h f org-timer-set-timer (org-timer-set-timer function help):
With two ‘C-u’ prefix arguments, use ‘org-timer-default-timer’ without
prompting the user for a ...
One way of going from an HMS form to the number of seconds is hinted by a line from the HMS forms page:
Dividing two HMS forms produces a real-valued ratio of the two angles.
So if an HMS form is on the stack
5@ 30' 0"
entering one second to the stack
and dividing by it
gives the number of seconds:
Not exactly a convert but it's only ...