That doesn’t sound right. Go to another independent shop for another diagnosis, avoid dealerships as you might get a similar sized bill. Research shops in your area via Google, Yelp, etc, good luck.

My opinion, take with a grain of salt:

I don’t know how a fuel pump replacement is over $1k, an OE Delphi pump replacement on RockAuto is $350, I find it hard to believe it’s causing all those lights on the dash. Where is the $650 is labor going to? That can be 5-9 hours of labor depending on the shops rate, which too much IMHO. The pump is under the rear seat, it can be replaced DIY in less than 1 hour, 2 hours if you take your time. Definitely get another diagnosis IMO.

That car is ready for the junkyard.

You didnt mention in the post if the timing was set when replacing the chain. Replacing the chain without setting timing can bend the valves in the cylinder head, the 2.4 ecotec is an interference engine.

As for P1682, that seems to be a seperate issue. The problem being the fuse box. This might help you if youre the DIY type: https://www.chevymalibuforum.com/threads/code-p1682-07e8-service-traction-eng-pwr-reduced-service-esc-the-car-runs-awfully.121470/