I actually had a conversation with a magnetic sheeting yesterday for a customer of mine. There is un-magnetized sheeting that can be magnetized after printing and in your case "scoring" with a plotter, with some sort of handheld device. The issue with that technique is that there's no way to know if you missed a section visually when magnetizing. So for my application, we need to find a solution that will allow printing/finishing traditional magnetic sheeting. There was a suggestion to secure a slip sheet of vinyl backing material with the slick side up on the metal surfaces that the material touches through the printer so that it will slide easier through the printer. The other suggestion was to attach magnetic material magnet side up on the front and back of the printer so that the magnetic poles are "pushing" against the back of the magnet as it feeds through. I haven't tried either yet, but these suggestions make sense.
As far as printing then finishing/scoring/cutting, the best possible solution would be to print using a flatbed UV printer, then cut out using a flatbed cutter... but if you don't have that equipment, its a big leap to justify the purchase unless the ongoing project could pay for it... which in my case it just might. Good Luck to you.