It does not make any difference if you check "Add PC drives at startup" or not, because WinUAE no longer includes CD-ROM drives with this option. CD-ROM drives must either be added explicitly or by uaescsi.device emulation.
I get alot of AMIGAOS3.9 has read errors
As told before this is a MaxTransfer issue. A restriction of ASPI as Toni Wilen said.
Boot again with this startup-sequence thing and without the emergency disk in DF0. Then insert the emergency disk. Open a Shell window (in Emergency-Boot/System) and enter
ed df0:devs/emergency_cd (I hope the editor works on this extemporized environment).
Now search the line that reads MaxTransfer = 0xffffffff and change it to MaxTransfer = 0xfc00
Then press Esc and enter X to save the changes. Enter Q instead of X to discard the changes.
Bye,
Thomas