I'm assuming you're removing the floppy drive when going portable. I know you're removing the HD. IIRC, the rest of the Amiga will work fine without the -12v. In fact I'm not even sure it will need the +12 with the HD removed. The CF card should run on 3v or 5v IIRC. The only sticking point would be the voltage conversion through the IDE-CF adapter. It wil be expecting to see a +12 and -12v iirc. Bypass that though and you should be good to go.
I think this is your best bet. If you don't need the -12v, no point in hassling over it.
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