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Intonation help

So I've got an Epiphone Thunderbird pro IV recently, and when setting it up I can't get the E and A to intonate. The saddle is out of travel but I only need a little but more. Any tips on getting a bit more travel without moving the bridge? The obvious solution in my mind is to cut the bolt and spring shorter to allow it to travel a bit more, but I doubt I would be able to clean those threads up afterwards on such a small bolt. Aside from those two strings, this bass was a breeze to set up and plays great
 

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Different strings may intonate differently. I'm having this issue myself with a J bass and a different brand of string fixed it.

Otherwise, I can't see the construction of the screw and saddle, but is it possible to cut deeper threads with a tap and die?
 
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You'll need to do just as you said, shorten those screws, and clip the springs. The blind holes in the saddles are a boneheaded design flaw, IMO.

As previously posted, threading a nut onto the screw before cutting will help clear the threads when you remove it.