How do I work with these "chunk" files? I don't see any way of writing them to a partition or being able to mount them as a disk image. dd maybe?

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I agree with Stu's post about checking the EIDE header on the empeg. I've fixed several with cold solder joints after going through the same frustration you're seeing. Drive goes bad, replace drive, only to find out it's a bad cable or cold solder joints on the header that started the problems in the first place. If you have have solder skills, this is a quick job.

The original HD is definitely bad. Plugged into my pc I was getting IO errors and have the files/partitions were completely gone. The solder points on the board look fine as does the cable. I certainly won't rule this out and might reheat the points after a few more things to try out.

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Another thing that has caused problems is using a USB to serial adapter. The driver tends to put the thing at COM 21 or something crazy, manually changing it to a lower COM port helps.

The serial adapter was working fine for both minicom, cutecom and hyperterminal under vmware. It shows up as ttyUSB0 which I map to com1 under windows. I have been able to flash dev kernels and hijack with it just fine. The problem i've been seeing is the builder kernel not building the HD.