Did you use some type of gluing caul on the inside of the guitar, against which the clamps were seated? Did that/those get removed after the clamps were removed?
If the bridge is adequately glued, there is no reason to remove it again. It is unlikely that the glue joint/how it was glued has altered the tone, given that you used Titebond. Also, you don't want to remove anymore of the top wood. Unless absolutely necessary, leave it alone.
As an aside, if a guitar top has runout, and most do, then the runout will be oriented in opposite directions on one half of the top compared to the other. When removing a bridge, that means one usually approaches the removal from opposite directions on each half of the bridge. That about half of the bridge has a fair bit of top attached to it, while the other half does not, suggests that, perhaps, you didn't approach it that way. (The half with top stuck to it, was removed in the opposite direction than it should have been.)
It is possible that a blob of glue in the saddle slot prevents the saddle from sitting flat. This would be an issue for an under saddle pickup, but wouldn't likely change the un-amplified tone much, if any. "Levelling" the slot isn't appropriate, if the problem is a blob of glue in one specific location. One of the most difficult things to learn is to correctly identify a problem area and work only that area, and not everything around it. Working the entire area, rather than addressing the specific problem, often makes matters worse, not better: one hasn't addressed the cause of the problem.
None of the things you've mentioned are likely causes of a significant change in the sound of the instrument.
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