the standard process in both cds is to make first an Emergency floppy disk, then boot from this floopy with the cd in the drive, and after boot, run the normal instal from cd. did you made this Emergency floppy?
why you bought both? os3.5 is part of 0s3.9 cd.
just use the 3.9. make the floppy and go on. what brand is your turbocard? do you have any ide/scsi extra hardware connected on amiga? sometimes this bring some troubles.
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here you can find more usefull instructions
