I don't know To add to the strangeness, it all worked perfect for the two years I've been driving the car. I only just changed out the transmission, nothing else, UGHH.

Does the negative cable go straight from the battery to the engine block?
Nope, The battery is in the trunk, ground to the chassis. I guess all of those Prothane mounts and shiny paint are good insulators.

I'm going to run to a parts store soon and get a couple of those ground straps and make sure the engine and trans are both attached to the chassis, and yes some paint will need to be sacrificed.