Hmmm. Sounds like you got a bit of a jam on your hands. From your description, it sounds like the old AMC 20 axle assembly on Jeeps.
I like WD-40 for lots of stuff, but for removing rusted-together stuff, I use <A target="_blank" HREF=http://www.gunk.com/autocat3.asp?pic=L112>Liquid Wrench Super Penetrant</A>. I'll admit, sometimes it has taken multiple applications over several days, but it does seem to work a lot of the time.
Not sure what type of gear puller you are using, but there are some pretty heavy-duty ones out there. Perhaps seeing if you could find one with a lower pitch thread (e.g. more pressure exerted) may help.
Last thing I can think of is if you can remove the axle shaft/hub assembly from the axle housing/differential as a unit, you could use a couple of things to remove the hub from the axle shaft. You could use a press (12 or 20 ton - like they sell @ Harbor Freight for $100-200). You could also try using dry ice and to cool the axle shaft. Once it's cooled use the press or gear puller. It's kindof the torch thing in reverse. Course, this works a
lot better for putting two tight fitting things together since you don't have any temperature transfer when the items are separate, unlike when they are together, but it's worth a shot.
Course, if the hub is stuck that well on the axleshaft, I'm a little curious why you wish to remove it. /w3tcompact/icons/hmm.gif (do you need to remove it to get to the bearings?) I'll admit, I don't know anything about Yanmars, just a thought.
Hopefully some of these ideas will help! Good luck!!!