Starter cable grounded on trans, le sigh... Options

[95CelicaST]

MR2V6 content, but subject matter is universal I think.

So yesterday while leaving my driveway my car shut down on me. When turning it back to the ON position my tach wasn't doing its sweep (LinkECU start-up). Then I saw the smoke coming out from the engine lid. When I popped it open I could see the smoke was coming from the starter wire. Apparently it had grounded into the shift linkage on the transmission and roasted my battery (that poor Optima )

Fast forward to this afternoon. I put a new battery in and it was very sluggish to turn over, but it did and started and ran fine. So I yanked the starter off and replaced it with a new unit... and the sluggish starting continued.

I am going to pull off the alternator and take it in to NAPA to get it tested/replaced... thinking the built-in voltage regulator might be fried on it. Is there anything you guys can think of that I am missing here? Or am I on the right track with this? I guess I've never roasted my electrical system before...