I couldn't find anything in the FAQ about this one,
so here's the deal. It's complicated kinda.

I just swapped two drives between two MKII's because
I had to, and now one of them totally locked me out.

It's a MKII running latest beta 11 consumer image
and whenever it boots it just sits there and alternates
on the rio boot screen between 'Initalise Mixer Failed'
and 'Loading Music Databases...'

Problem is, that using Emplode and/or JEmplode I
cannot get into the player. It won't see it on
ethernet or Serial (USB is out I'm on XP) when
I power it up and boot it and I know that's like
BS because I can connect to another MKII with the
exact same configuration by doing the same procedure.

So, I'm really confused. If the thing is stuck
booting up because the software is messed up
either because I swapped disks or the MB perhaps has
the wrong firmware, etc... then how can I get into it
to upgrade the software or flash the kernel, etc...
and get this thing fixed up???

Quite the pickle.

actually, I just used the logo editor's kernel updater utility thingy to install hijack and that solved the problem I think. Hmm... to reset the unit to factory settings what kernel image would I install for a MKII?

hmm, ok now after the thing boots up it shuts off and won't come back on no matter what buttons I push and the remote won't work. Dope. Rough morning my way.

You probably have a firmware mismatch. 1.03 kernel on flash and 2.0b on the HD or vice-versa.
Just do a regular firmware install.

Exactly, that's what I thought to. So that's what I did. However, although I can talk to my empeg and connect to it and transfer files and what not it is still acting strange.

For some reason iit still just boots up, shows the normal boot sequence on the screen, hard drive chatters, turns itself off and then like dies. The remote won't work and the unit's controls on the front panel won't do anything. It's the wackiest thing I've ever seen...

Get a serial log from the player. See the FAQ for instructions.

The instructions for getting a serial log are here.