Loch-  
 
Try a soft rag to apply the lemon oil- then use it to gently scrub the ebony.  That's what I've done on several of my other basses and it's worked well.

0000 steel wool works really good. Just cover the pickups so that they don't attract the steel wool dust. I usually put some masking tape over the pickups before I do this. I detack the tape slightly by first applying it to my jeans so it won't do any damage to the finish. You won't need to rub hard with the steel wool, and it's not too abrasive to damage or scratch the inlays. Just work in the direction of the grain as to avoid any visible scratches - a little harder near the 2nd octave where you really want to go the direction of the frets. Best method I found is to use a little oil with the wool to wet sand which will minimize any scratches but really pick up the dirt.
Kris

You can also use the synthetic steel wool (most people I know call these green scrubbies).  Non-ferrous == no problem with sticking bits to the pickups.
 
This was the recommendation that I got from James (at Alembic).  You can get them in the paint department of your local Home Despot.
 
I usually just use lots and lots of Q-Tips, and sort of scrub the ebony to get the funk out.  I usually put a little bit of lemon oil in each.

I use whisky and old cloth diapers and high quality q-tips.

Where exactly does the whisky go? On the diapers, on the q-tips, or in you?

Thanks to everyone for the advice! It seems to have cleaned up very nicely. I think the fret ends may still need some work though.

This is from the Owners manual. I've had it happen on both my fretted basses the first winter. I just filed down the ends myself.  
 
You may notice that the first time the humidity takes a big swing that the fret edges may protrude over the edge of the fingerboard. These can be easily filed flush and you will probably only have to do this once. You can get a service sheet from us if you'd like to do this job yourself.  
 
Keith

My wife is a perfumer and aromatherapist, so I just hit her up for some aromatherapy grade lemon oil. It works well and a bottle lasts forever. A while back she did a discount for Alembic club members and I bet she'd do it again.
 
Edwin

My guitar has an extravagant dragon inlay. Is there any special procedure I need to follow for oiling/cleaning a fretboard like this. I feel a bit of dragging when i'm fretting which I don't get on a plain ebony fretboard so am wondering what to clean it with.
 
Cheers
Jazzyvee