I smelled something burning and thought I had a flat but, it seemed like it was the brakes -back brakes locking up...I drove it home but, now what??

Assuming the it was definitely a failed pump that was the reason for the swap?

It's a while since I had the XJ6 Sovereign but this is where I'd start troubleshooting.

1. verify power feed to the pump: Check the Inertia Switch hasn't tripped. Check power to the pump relay. Check the relay. Check the power feed at the pump.

If this checks out OK then,

2. Fuel feed: verify fuel delivery to the fuel rail. Verify fuel pressure at the fuel rail.

If you've handed the repair shop a Haynes manual, they'll find all the above procedures included.

If that all checks out and fuel is being delivered, it's on to the ignition system. The guys on the XJ40 section will have the schematics for this.

Graham