I've done it only once, but it was under the watchful eye of Lee Von Erck, in his shop. I was reasonably pleased with how it turned out.
If you have a belt sander, you can start by getting it closer with that. It'll save a lot of filing. But watch your angle of attack constantly and vigilantly... if any shank briar touches the belt, you'll never get it back!
Once the ebonite is maybe credit card width proud of the shank (at least!), start filing.
You want to do this with the stem fitted, of course, so that you can work it custom flush to the stem.
Lee taught me to put a little block in front of me, like a hunk of 4x4, with a plush towel draped over it. This allows you to turn the pipe down (or whatever angle) over the edge of the block, while the stem/shank rotates in place, so that you can easily work around the underside, etc.
Your first job is to get the fit flush. You can worry about the stem shaping later.
Angle of attack is everything. The file must remain perfectly parallel with the shank. If you dip down towards the shank at all, you'll take away briar that you can't get back. If you keep the file parallel with the shank, and are patient, you'll eventually get it flush.
As for shaping the rest of the stem, it helps to have a finished stem in hand which you're attempting to imitate. If you take things slowly and figure it out as you go, and patiently keep working towards imitating the model stem, you'll get kinda/sorta close.
These molded ebonite stems do still need the slot cut ... they come with just the round draft hole. Lee did my slot with an electric reamer, so I can't help you there.
For finishing, just work to finer and finer grades of sandpaper, eventually to micromesh... I actually finished with a Mr. Clean Magic Eraser. Just take it in systematically graduated stages to the finest stuff you can get.
(If you finish with Obsidian Oil, you'll feel like a real pro ;-) )
I did mess up a bit and take a tad off the briar -- both in filing and in sanding. But I just grabbed a pack of stain markers from Home Depot, chose the closest match, and voila! -- you'd never know.
Let us know how it turns out!