First off, great choice of head unit. I'm a big fan of Nakamichi, and doubt I will ever own much else
I don't know the older 6er layouts, but I did have a similar dash mounted fader on a previous car (1986 Porsche). I didn't need to bypass it, as it was had a built in impedence matched circuit.
I could speculate on the wiring, but couldn't tell you for sure. You can use your amped (not preamp) outputs to feed the oem amp, as the Nakamichi has a relatively low voltage output via it's speaker leads. That is currently what I am doing, and have had no problems. That hi/low inverter you posted from crutchfield is a good product, but not necessary in this instance.
If I were in your shoes, the first step I would take, would be to purchase four new speakers. I'm sure your oem drivers are in pretty bad shape, and even if they aren't, they are not capapble of taking full advantage of your new head units ability.
Once you have your new speakers, you can use your existing speaker wire, you just need to find the leads that run from the dash area to each speaker location (you said they didn't match, something should).