Pinion marks disappeared

[abohler1]

So I made all of the proper pinion marks for a seal replacement with a paint pen. Now that I'm putting it back together I'm not confident the marks held up. Many threads appear not to have marks any longer. Am I screwed? If I'm close should I be good? The nut still has the marks and so does the top of the shaft, but just not sure how many threads to take the nut. Can I line up the lines and torque it to factory spec? Thanks for the help.