Hi Brent, couple of ways. You can practice on a piece of scrap plywood and when you are happy use that piece as your template to cut it into your box top. Or, if you don't have access to the inside of the box to mount the pickup into the lid, then tip #2....
use your new template to to make a plate/surround out of hardwood or plastic pickgaurd type material, mount the pickup in that and then mount the whole assembly into a less tight a fitting hole in the top.
Got pics if you need them but I think you'll get my drift.
Hi again Brent, I see that I did not see your photo or answer your question fully.
To make a template that you can use over and over, draw a line left to right and place the pickup on the line with the screw holes on the line and mark and drill the bolt holes. I would then turn the pickup upsideown and put the bolts in place and into the pickup. This will hold it in place while you mark around the top face of the pickup.
Then it's carefull sawing and filing to get a close fitting hole.