Can quantum algorithms with exponential speed-up be rederived using span-programs?
I guess there are at least 3 questions in your question. I don't have a satisfactory answer to all of them, so this isn't a complete answer. Hopefully there will be more answers that answer all your questions.

The question in the title: Can quantum algorithms with exponential speed-up be rederived using span-programs?

As you noted, the general adversary bound characterizes the quantum query complexity of all decision problems, including promise problems for which we have exponential speedups. So, in principle, there is a span program that solves the Abelian hidden subgroup problem, which is the query problem used in Simon's and Shor's algorithms. But whether there is an explicit span program for this is your next question.

Is there any work re-deriving Simon's or Shor's algorithms in the span-program framework?

I haven't heard of any such results. I don't know of a span program for Simon's problem or any other AHSP.

Is there a way to translate polynomial-method lower-bounds to general adversary lower bounds?

Yes, I believe there is. I can't seem to find the paper that has this result, but I can give you a link to a talk given by Jérémie Roland. In the abstract of the talk, he says the following:


  ... More precisely, we will show that the multiplicative adversary method, a variation of the original adversary method, generalizes not only the generalized adversary method, but also the polynomial method, so that it essentially encompasses all known lower bound methods. Therefore, this provides a constructive approach to cast polynomial lower bounds into the adversary method framework.


Update: The paper is now available online:
Explicit relation between all lower bound techniques for quantum query complexity by Loïck Magnin and Jérémie Roland