Show the part to your Indy guy. The starter can't possibly damage the windows, only starter ring gear teeth and that'd also be obvious BUT damaged ring gear teeth would only cause intermittant starter engagement problems or noise, not stalling. The RPM sensor/ECU doesn't see or care about starter ring gear tooth condition but does need those windows to all be there and readable.
There's an inspection hole on the firewall side of the trans bellhousing towards the top that should have a rubber plug in place. Chances are good that someone used that hole to place a pry bar or large screwdriver in to hold the engine from turning while removing and/or installing torque convertor bolts and that'd be how one bent those window openings. That's NOT how one should ever try keeping an engine from turning over. The part is proof of the damage.