Not sure if I really understand what you are trying to do, but it doesn't seem to be related much at all to fine scale modeling. There might not be many people on here that can offer good advice.
Your dimensions are a little confusing. You said it was 5mm (as in millimeter?) thick acrylic sheet. Seems to be that your slots are 2 millimeters wide and 5 millimeters long, drilled into the side of the sheet. Those are very small dimensions. Very careful masking of the faces (inside and out) that you don't want painted might allow you to spray paint the remaining face (at an angle to the slot opening).
But you also say you have "about a thousand" of them. If that isn't an exaggeration, I don't see how you can do it fast AND clean. You'll have to pick one and sacrifice a little on the other, you can either do it fast, or do it clean, but not both.
Paul