What should I do to clear my conscience for selling a merchant's goods at a higher price than he specified without his knowledge, and is it permissible to give charity on his behalf instead of giving him the money?

What you have done falls into two categories:

The first category: If the merchant said to you, "Sell for such and such, and whatever exceeds that is yours," then this has two situations: 1. If there is a known commission other than the increase, then there is no harm. 2. If the commission is the increase over the specified price, this is a point of contention; the majority of scholars hold that it is impermissible due to the ambiguity in the commission, while some scholars permit it, and this is the more sound opinion.

The second category: If the merchant said to you, "Sell the item for me and do not go below such and such," and did not say, "whatever exceeds it is yours," then in this case, you are an agent, and the increase belongs to the owner, and you must return it to him, and if you cannot return it explicitly, then do so indirectly.