I can agree with most posts here. I'll chime in on a few.
Balls: I've seen lousy ones come in NIB Sterns. I've also seen ones that looked perfect that I tossed because I was nervous about the past lousy ones. No brainer at a very small price. I've been happy with Ballbaron.
Protection: While it's never a bad idea, I'm not sure it's necessary on a home use game. Your drops probably already have mylar from the factory, magnet and shooter lane wouldn't be a bad idea. If the game had a scoop I'd be buying a Mantis protector.
Color DMD: Not only adds a lot to the game, it's easily reversible and works on tons of games. Pricey at $400 plus shipping. I think it's worth it.
Invisiglass/PDI Glass: If I could afford it every pin I own would have it. Again, if you sell the game, put the original glass back in. It will work in any standard width game. Expensive.
Shaker: Short money, easily reversible, works in many games.
Aftermarket Speakers/Subwoofer: In a 1 pin collection maybe. Stock speakers don't sound bad on this game. I've upgraded a bunch of games speakers and added a sub to Metallica. Certainly don't notice it much when 4 or 5 games and a jukebox are on. Headphones sound better than any of the speaker upgrades in my opinion, though I don't find myself using it that much.
Cup Holder: Such a great idea. If you are a pinball drinker buy one for every game.
Side art: I like the side mirror or mirror blades. I put them on almost all of my games. Any game I've had with side art it ends up getting torn. Side mirrors get scratches, but nothing compared to a torn decal. These will leave 3 tiny screw holes, somewhat reversible.
I would stay away from playfield mods and toys. They can get expensive and typically add no value. If I'm buying a game and it has extra figures all over the place I'd just be wondering how I can get them all off. Everyone says the Vengeance mod is great, this may be an exception.
Other than the balls, none of these are necessary to enjoy the game. And the balls may be fine. I wouldn't hesitate to play the game until the new balls came in unless they visibly look bad. Clean the oil off the balls, give the playfield a quick wipe and inspection and enjoy! It's an awesome game.