Whoa, hold up! The hub is pressed into the bearing, and the bearing is pressed into the spindle. You should know this, if you already did one side. The axle should not be stuck in the hub. It's just splined. A little PB Blaster at best. The axle can't really push in until the spindle is swinging loose on top, allowing the spindle to come out, not the axle to go in.
Also, you have to be REALLY careful using tie rod or ball joint separators on this entire job. These joints don't have a flange to work with those separators. In other words, you'll destroy the rubber boots, and I don't think you can buy them separately. Which means you'll be buying the joints (ka-ching). The best way to deal with them is to soak the heck out of them (overnight?) with pb blaster, and whack the sides of the joints with a big baby sledge hammer. There's nothing holding them in except corrosion really, not so much pressing. So it's the shock of it, along with the penetrating lube, that does the trick. The rear tie-rod was somewhat of an exception. You can use a separator, but not in the traditional manner. I used the fork on the edge of the joint, not around the middle. In fact, I ripped one boot trying that. And it was not available separately. And the universal aftermarket one I bought in the HELP section failed quickly thereafter.
On the upper ball joint, I vaguely remember smacking the spindle with the hammer. A little hammer wont get it. You need a baby sledge or a deadblow metal hammer.
Back to your main problem, be careful not to hammer the end of the cv axle, or you could distort it. Just pull the entire rear knuckle off the car, with the hub and bearing still in it. The axle should slip out the back of it easily. If it does get stuck, you might try putting the nut back on the axle, flush with the end of the axle, and use a piece of 2x4 wood, and give it a tap with the sledge. I said TAP! The cv joint will NOT tolerate beating that axle in.
