Remove all of the top plastics so your playfield looks something like this, except leave all of the red post intact and remove the rubbers, only the large ones touching switches. Try to lay them on the playfield so you know where they go back on. Also, don’t worry about the pop caps. This will only take a few minutes to do and make it easier for you to see all of the switches. Don’t worry about the top apron or bottom apron either, this just happen to be the only picture to show you.
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Start up a game and see if you are still having problems. Activate each switch by hand and see if they score correctly. If you are still having issues, turn off machine and inspect all of the switches. If you have some fat straws, slide one over each switch as I have highlighted here, make sure it goes all the way down to the bottom. Start the game again and start pulling the straws one by one. If the score reel locks on, you have found your switch. If you are having no issues, start putting the rubbers back on one by one while the game is on.

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Should look something like this except in this picture I am covering the whole switch. In your case you only want to cover the first blade as pictured above.

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Whole process should take less than an hour, Super-Flite is not that complicated of a machine. Don’t be intimidated thinking it will take all day, you’ll find it.