I'm running a coundown timer and I want to mask out the first (hour) number.
I can't figure out how to make a working mask. I have tried using a shape and the pen tool, but it doesn't hide anything.
My layer is set up as New Layer Solid> Effect Text>Numbesr>Type Timecode 
when I do a shape over another layer, it masks fine, BUT I can't for the life of me get a mask to work over this text.
The part that's relevant to you right now is that masks are rendered before effects. This means that the mask is not operating on the result of the effect that you've applied.
The way to take control over the render order is to precompose. In this case, you could precompose the layer with the effect and then apply the mask to the precomposition layer.
Given that you're new to After Effects, I very strongly recommend that you start here:
Two options. First, Precompose your Solid with numbers effect applied making sure that you check Move All Attributes . . .
Second, and possibly better, use a text layer and an expression. You'll find a bunch of options on Dan Ebberts site by following This Link. There are several advantages to using text layers. With each solution make sure you use a monospaced font.