Be careful taking out the saddle. The Tune-o-matic bridge has retaining clips or wires that keep the adjustment screw from screwing out of the bridge. You don't want to lose them or forget where they go or how they go.
Your pic links still don't work but I would try to lower the bridge on the E,A,D side of the strings before tinkering with the saddles. As you mentioned it seemed were a bit too high. Make small adjustments, and test.
Michael
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