I hope these tips saves you some time and heartburn on your repair. The 2 games I learned from were Black Knight and NGG, but the tips should be applicable to other SS games.
1. Protect the game. If you zapped your CPU or blew a fuse, don't re-install the GI connector until you've figured out the problem! This means (a) figuring out which GI string is shorted, and (b) fixing the short.
2. Visual inspection. Get a nice bright flashlight and a magnifying visor. Look at the bottom of each socket. If the "tit" is touching the base in any way, bend it back to resolve the short. This is also a good time to look for future trouble spots. If you still have a short after inspecting and adjusting all of the sockets, get on the top of the playfield and look inside the sockets. On my NGG, the culprit was a tiny sliver of metal sitting between the base and the spring. It was so small I almost missed it, even looking right at it!
3. Isolate the bad GI string (part 1). The GI strings are "paired off" as they move through the game. On my Black Knight, only pins 4 and 8 were a dead short. To figure out where that GI string went to, I pulled pin 8 out of the connector, plugged the connector in and plugged the game in. The backbox and coin door lights came on, so I knew the problem was on or under the playfield. This is what it looked like - the burn marks point right to the 2 pins that were shorted!
4. If possible, remove all bulbs from the suspect GI string(s). Then you can use the diode setting (see next tip). It's easier to debug with your ears than with your eyes.
5. If there are ANY GI bulbs still in the game, you MUST use the multimeter's OHM setting, not its DIODE setting. A #44 or 47 bulb only has a resistance of 3-5 ohms. On my cheap multimeter in "diode test" mode, 5 ohms was low enough to trigger the "beep", making me think I still had a short. I drove myself nuts chasing a short that I had already fixed!
6. Isolate the bad GI string (part 2). If the GI string is really long (often the case on older pins), you can "divide and conquer". This was really easy on BK, since the upper and lower playfield are connected via Molex plugs. I disconnected the lower playfield, and the upper playfield tested good. This narrowed down my list of suspected sockets considerably. For games without any plugs, you can temporarily unsolder one or more "substrings" until you find the bad one.
7. Once you've narrowed the short down to a "substring" of 1-6 bulbs, go back and do another visual inspection. If you still don't see the problem, unsolder each lamp socket until you find the bad one(s).