"Firstly, if anyone has any advice on touching up checkering, I'd love to hear it, never done it before."
Well, if you're going to ignore the advice to hire a pro or at least practice on a throwaway, then....
1) Start with the attitude that it's going to take you a long time and 4-5 passes with your cutter to complete the job. If you get tired , impatient, or (worse yet) cocky, stop and give it a rest. Set your cutters to cut on the PULL. Start by placing your cutter just inside the near border and push 1/2-1" towards the center. As you push, you create a dented or slightly scratched line that your cutter will follow on the return. If you make a mistake on the push you can stop, lift the cutter, and start over.
I've checkered and recut dozens of stocks and NEVER used a cutter to cut on the push. And though I've seen it advised, I've never seen the reason explained.
2)As you advance from the near border to the opposite border in a back and forth motion of 1/2" steps, stop 1/4-3/8" short of the opposite border. When you've covered the entire pattern, and left an untouched 1/4" wide border, you can now tackle that last bit as a separate task.
3)Starting at the border opposite you, place the tip of your cutter at the border and gently PULL away from it, towards the center of the pattern. In other words, never try to run up to the border from the inside of the pattern, and you'll never runover.