well, I don't have a lot of time right now, so I will just say that I will provide my in-depth thoughts on this rear suspension later on, after I get home from work.
As to converting a cobra to an automatic trans, personally I would advise against it; but it could be done, though more than likely it would end up being a hack-job, especially considering you would want it to be a daily driver type vehicle, rather than a drag racer. This would warrant a modern electronically controlled trans that is capable of supporting the power output of the Cobra engine. (not too tough to find a beefy enough one for a 99 or 01 I guess, but good luck on an 03)
another thing to consider with that, is that the Cobra PCMs have no provision (at least software wise) to control an electronic auto trans, so either custom programming or a custom trans controller would be required.