You say "putting some bomb bay doors on a modern Boeing" as if that is something that you can just do without redesigning the entire aircraft. Some other the changes you would need:

- Retraining the entire fleet of pilots for the new aircraft.

- Recertifying the entire set of currently available weapons that the B52 can drop.

- Integrating modern military radios/crypto/satcoms/datalinks/etc with the civilian Boeing system.

- Replacing all the spare parts/simulators/ground equipment/etc.

Now these are not unsolvable problems of course; all that gets done every time a new aircraft model is introduced. But there is just not really a need to replace the B52. The main downside is that it's a bit of a gas guzzler, but apart from that the USAF would gain very little in capabilities by replacing the B52 with a modern airplane. It would be very expensive for basically no gain.