I've solved it!
The problem was a rather trivial one: The Windows disk had SCSI ID 0 and the Linux one had ID 2; apparently the computer correctly read the boot sector of the Linux disk when I set the boot ID to 2 but Linux then identified sda1 not as the booting disk but as the first disk with an SCSI ID and therefore tried to check the filesystem on the Windows disk. I just switched the SCSI IDs and now I can at least boot either OS by choosing the boot device in the controller setup (Windows doesn't mind to be on ID 2).
I've also got file reading and writing access between the harddisks both from Linux to Win and back.
Next I will try and edit lilo.conf so that it includes the Win boot option, so that I don't have to switch it on the controller anymore. I'll be going by the Lilo-HowTo on control-escape.com first and be back if I fail. But I feel more confident by the minute, especially as the new disk killed my access to my parallel zip drive (which had previously been sdb4, now in conflict with the new hd) and I managed to edit fstab so that the ZIP already works again. One of these days I'll know my way around this OS, too