So if you have to really dig in to remove the rust, you're also taking out base material. Just food for thought. Even something heavily rusted can shine up with enough sanding.
That said, your biggest source of flat tappet failures these days is lifter faces not properly ground. There's a guy in YouTube, Powell machine inc, he does a good job explaining what's going on. Worth considering sending your lifters out for a cleanup pass especially if they're newer.