My machine is on firmware 3.10 allowing for bulk ink and constant access to service mode from the setup menu directly. If you mess with anything, don't expect to get a good result without reading the service manual (available on the yahoo user's group) and using some magnification. There is a great little illuminated "microscope" thats available at radio shack that some of the yahoo group guys have recommended and I have been happy with it for the price.
As far as media comp goes, most manufacturers recommend that you do a quick test every time you load up media. You'll also find on really long print runs that you'll have to chase it a little.
Finally, the media comp print test is intentionally not very opaque and its very "bandy" its not a problem with your machine. It actually makes it easier to see the adjustment under magnification.
The regular users manual deals with the media comp and other non-service menu adjustments. Its worth reading. The service manual IMHO is mandatory mimaki reading.