How can one find an element in a Merkle tree?
Merkle trees are not designed to support efficient lookup.  The best you can do is search the entire tree (all the leaves) and check each node for a match.  This is $O(n)$ time.

If you want to be able to efficiently look up an item in a Merkle tree, construct a separate "index": i.e., a separate hashtable (or binary search tree) storing the mapping from hash value to position in the tree.