Ah! The culprit was slightly bent pins, pin 1 and the one above it, so that there was no contact. Once I straightened them out, everything was normal. First I put the HD floppy in alone, A3000 boots normally. Then daisy chained the original DD floppy to the HD floppy, and the 3000 boots normally.
Then, I tried formating some disks in the HD drive. If I put a HD floppy in, two icons appear. Choosing format from the menu from DF1 let me format in 880k, choosing format from MS1 let me format in 770k. But, once you did format, it only ran for 3 seconds before quiting. An error message came up saying that it couldn't initialize.
Where in WB, do you allow it to format at 1.4m? Is that something in the tooltypes? Why would it quit after you start formating?
Although CLS2086 has some good advice. I think my DF0 drive could use some maintenance. Half the time it works poorly.