For my layout, I will have two screens - one with the presentation and one with my notes. I would like to set up a timer on my notes screen, large enough that I will be able to see it by only glancing at the screen.
It sounds like you intend to use Presenter view. One of the things that appears on the notes screen in presenter view is a timer.
It won't tell you how far off your "target" time you are but if you put the target time in your notes -- ie, you should be done with this slide by no later than XXX elapsed time -- that'll give you the info you need.
It's probably possible, with a lot of flailing about in VBA, to add a feature that checks the target time against the actual time that you land on a given slide and adds some kind of cue to the notes text, but with the top line of the speaker notes and the existing timer right next to one another, there doesn't seem to be any need for this.