It seems that any attempt to execute a program from the CD fails. It also seems not to be limited to executing stuff - I had this error too:

Unable to open Which for input: disk is write-protected

when trying to copy a file. I shall keep at it and report back if I get anywhere.

Maybe the AmiCDFS filesystem doesn't like linux or something. Try to copy everything from your CD somewhere to harddisk and add "AmigaOS3.9" assign at the beginning of the amikit startup-sequence.

Well, I did it! Here's what I needed to do:

* ditch the Debian version of UAE for E-UAE (http://www.rcdrummond.net/uae/) due to a segfault while installing AmiKit and lack of a JIT compiler
* copy AmigaOS3.9 CD to the hard drive and make appropriate device mapping in UAE
* make sure everything in AmiKit: is executable
* add a line to the startup-sequence to set the pure bit for the CopyReplace program or it won't go resident

After that, it was pretty much plain sailing. AmiKit installed 3.9 and I applied the updates and Boing Bags without trouble.

nice, congratulations! :)