I'm sorry you're having trouble w/your down timer. I'm not sure I understand what you expected of the timer (perhaps you wanted an uptimer?) but I'll give you an example of how you might use one for your situation as I understand it.
I have a little sample chart with my downtimer_1 (like yours) and timer_preset (a float). Both could be part of your PAC Display project, one for the user to put in the 40 minutes (or some other value) and one for downtimer_1 which will run down from that 40 minutes (2400 seconds) until it gets to 0 as it counts down.
In my strategy, I loop, check the temperature, and when it's hot enough I call "Set Down Timer Preset Value" to timer_preset then "Start Timer" on that downtimer_1. I then loop through a condition block, checking if "Timer Expired?" The False exit goes to a delay, and checks again. True goes back to my hot enough check.
I hope that helps!