Yeah, I have (KISS). Kind of sucks.
The most important step is PREPARATION. Strip everything off the topside, fix any divots, bumps, etc as they will show up pretty easily, and take your time putting it on. If your replacement has the holes cutout for the lamp plastics on the playfield, it will be easy to line up. But if it doesn't, and those feature lamps spots are printed on the new overlay, then consider replacing all of the playfield inserts with new clear ones to get maximum light passage. It also gives a crisper look as you don't have to numbers or words on top of each other that might not line up perfectly and will look a little blurred. It will also make your playfield smoother as those inserts sometimes become a little concave over time from bulb heat.
And if you're worried at all about making sure everything gets repopulated in the exact same spot, take a bunch of pictures before you start...