Great composition and a great mix!
Don't worry what Herrmann would have done. You didn't claim to copy him...
I don't think at all that the timpanis are misplaced. The only thing I would change is the velocity of the single strokes. Of course it is possible to strike a drum that hard, but I would do this only for a single tutti beat in fortissimo, but not for a rhythm that lasts several bars.
If you make them play piano or mezzoforte, you will still hear them (if not, turn the volume up a little), but they won't disturb by being too much in the foreground.
For example, at 0:36 they could be much softer and there would still be enough left of them.
At 0:32 I could imagine a tiny roll with crescendo to "introduce" this first timpani note.
The strings in your second version indeed sound very warm and romantic. But to me it seems that in the first version they had better dynamics...
Regards,
Klaus