Sounds like you've been through a battle! Thanks for keeping us updated.
There are a few people on this forum that use CF cards, they may be able offer you advice in getting it working better.
As for the microdrive, interesting. I wonder if anyone else has got one up and running? Amiga.org or AmigaWorld usually have some technical threads regarding Amiga hardware - might be worth a look if you haven't already.
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