The first sentence is not idiomatic in its combination of tenses:
I have done as you had told me. NO
The past perfect, had told me places the past action, the telling, in relation to some other point-in-time in the past, whereas the present perfect, have done, places the past action, the doing, in relation to the present.
It is as if the parts of your sentence are standing back-to-back, preparing to duel.
I did as you had told me.
I have done as you told me.
Another very viable option is:
I did as you told me.
Another way to express the issue: a time phrase that relegates the action to the past is incompatible with the present perfect.
as you had told me interposes an implied reference point in the past, a point which the telling predated; as such, the telling is being confined to the past; it does not impinge upon or include the present, and this confinement-to-past makes that phrase temporally incompatible with the present perfect.
P.S. Compare the following:
As the specifications require, we use|have used stainless steel
As the specifications required, we used|have used stainless steel
As the specifications had required before they were revised, we used stainless steel fasteners.
we have used is not idiomatic with the sentence involving the revision to the specifications, because the past perfect confines that revision to the past. We would expect we used there, for obviously our use of stainless steel fasteners is pre-revision.
As you had instructed us before changing your order to vanilla, we
have baked you a chocolate birthday cake.
That sentence makes no sense. If we knew that the order had been changed from chocolate to vanilla, why would we have baked a chocolate cake? The only way to have it make sense is to say we baked, putting the baking before the change to vanilla.