This is the bit I was remembering from the FAQ. In the absence of any other input or explanation for why the 800K drive is accessing so slowly, something as simple as this could be causing the problem. However, I suspect it is some far more complex Lisa-ism that is at fault as do you, but when you are screwing around with non-standard configurations you have to try everything. Or just table this project until you get that replacement 400K drive.
"Technical Explanation: The Lisa floppy disk controller (FDC) anticipates 5 bytes of "bit-slip-FF" to synchronize its state machine to an address mark or data mark. The Macintosh FDC was improved to need only 3 bytes of bit-slip-FF, however use of this improvement was only implemented in the Macintosh II ROM and later.
The result is that some sectors of a disk written by a Mac II or later may not be readable by a stock Lisa FDC. This includes disks initialized on such a machine, as well as any file/directory data written on such a machine."
This is an interesting article regarding the differences between the Apple Unidisk and 3.5" 800K drives. If interleave is a factor, what I get from this is that perhaps because the 800K drive controls its own speed, that the Lisa does need the ROM in order to read the data at the correct speed, whereas the 400K drive takes its speed from the Lisa clock, which is presumably running at a different (slower) rate than the Macintosh clock due to its 5MHz processor vs, the Mac's 8MHz. Anybody know for sure?
http://www.apple2history.org/history/ah09.html#03