The original Sony drives should work fine with the Rev. B ROM upgrade and up. Check your drive against this tech note. Confirm which yours is. Based on Apple's description, I would imagine that the later drives were not always labeled properly.

The key now is to test your drive on another Mac. It does sound like the SE should otherwise function properly with the 400K, but you never know. There could also be something going on in the 6.0.8 System. Is it a clean System?

A 400K drive will not work on an SE 30. Don't plug it into any SWIM-based Mac.

The cabling only applies to internal drives, and only some 800K drives at that. External drives are already configured properly.