Sounds like something is causing the ready line to be pulled low when SEL2 is polled during power up, casuing the system to think there is a DF2.
Perhaps the faulty internal drive is causing these problems. Or perhaps the there is a problem with the floppy controller, which is why neither of the two drives are working correctly.
If you haven't done so already, check Paula (U400) and it's socket for corrosion, as it's located right beside the leak prone RTC battery.
It's also worthwhile swapping the two CIAs over as one could have an I/O pin problem. If the floppy starts working, but the parallel port or something now fails to work correctly, you'll know there is a CIA fault.
Reseat all the socketed ICs on the motherboard, as IC sockets are bad for developing intermittent problems which can cause strange things to happen.
Other than that, I can't think of any other reasons why the external drive won't work on the A3000.