Mine had this issue when I got it, but it was also exhibiting other strange behavior (losing track of which ball it was on most notably). In my case, the fuse block was the problem, and while it appeared the fuses were in tightly they actually did not have good connection and so there was some intermittent behavior. All the scoring/tracking issues resolved when they were tightened up. My other thought would be the batteries (in my case we'd already changed to an external holder and were still having issues).

Only part that has frustrated me in terms of acquisition are the white octagon stand-up targets. I have a broken one that I'd like to replace but they seem mostly out of stock (at least in that color). I think I saw a place in Canada with them, but since mine still works (just doesn't look great) I've held off.

I really lucked out on Superman; the person I got it from said he got it from another home owner in 1981 and had kept it in his basement ever since. The wear on it suggested it was on location at some point before then, but I was surprised at how nice it looked given what I was expecting when I was told it didn't work right (it was free, so I really expected a total train wreck).

My high score is 542,980. I believe I have special set as a 60,000 point award. Extra balls were enabled.

Yes, I almost went for it but while the photo was of 3 the narrative indicated only one target. Sold before I learned which count was accurate.

I put LEDs in the GI and backbox. Just white ones I had leftover from other projects. I like the games brighter for playing in the dark. Never tried the inserts (I know Gen 1 Atari used warming current so LEDs are a no-go, I saw a few of those in the backbox on Superman, despite being Gen 2 I guess they used it sometimes, and didn't want to mess with trying to get the inserts going since I have nothing around non-ghosting and the GI was what I really wanted brighter).

I used Comet brand. All frosted. I try to use warm white under the warmer colors (reds, yellows) and cool white under the cooler colors (blues, greens). Their sunlight white option works good under everything (I've used those exclusively on some other backglass swaps I've done), but honestly I think any shade of white is safe. I think cool white throws light the farthest, and I know others who always use it for GI for that reason, regardless of the color of the plastic above.

Any white will look clean. No clown puke risks.

The PinWiki guide on Atari machines does talk about this. I'll put the link below, but the warming circuit issue was a Generation 1 trait that couldn't be circumvented (well, without changing how you power the lights). Since Superman is Generation 2, they can be done (it mentions the dip switch):
http://pinwiki.com/wiki/index.php?title=Atari_Repair#LEDs

I've been meaning to get around to doing the rest of the playfield, I only did the backbox and GI (I was a bit short on LEDs at the time).