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Nick JD has got it right - with bridges like TOM or the Jazzmaster type from the Bigsby kit, which have much less range for intonation setting, usually you set the saddle for the high E almost as far to the front/neck as possible, and place that saddle 25.5" from the nut (or 12.25 from the 12th fret, which makes measuring easier), then mark the hole for the bridge stud on the high E (with your kit, the other stud will be at the same distance - with TOM bridges, the stud on the bass side is usually a bit farther back).
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