So I haven't updated this yet, motor is out. New motor has a broken timing chain cover, the alternator bracket is cracked, so I pulled the timing cover off the dead motor. It too is... unusable.
So I pulled the covers off both motors, like I said the cover on the new motor has a cracked alternator bracket, which is unfortunately cast into the cover and the old motor the cover is destroyed.
Ordered a new cover from a junkyard on car-part.com for $40, arrived and looks good.
With the cover off on the "new" motor the U shaped center timing guide is cracked up. So at the risk of dumping more money into a $600 car... I bought a timing chain, and timing chain guides for around $250. A friend has all the cam locking tools. I think if I'm doing the guide I may as well do the chain, its good insurance for the few months I'll drive it, and it should make the car much more desirable when I sell it as craigslist in Columbus at least has four M62 powered cars listed as "needing a chain" and reading online 100-120k is fairly common to be due for U shaped center guide. Its a $1,500+ service so I think it adds value to the car.
In other good news the transmission has a rebuilders sticker on it, and a bright new torque converter with 8/2013 written on it.