Hopefully the only problem with your new-er axle outer joint is the crack in the boot. If so it should be pretty easy to make one good axle out of these two.
Make your good axle from these parts-
Old axle's two boots and inner joint
New axle shaft and outer joint
To change boots or inner axle joints, you need to first remove the metal boot clamps. I found just putting needle nose pliers under the clamps and twisting to break them works. For the ones where you wont' be using that boot, you can hack saw through the clamps.
Now that the boots are free, pull them back from the joints a bit, and be careful of the thin grease spilling out. Just take the inner joint case and slde it right off, as the boot is the only thing that even holds it on. Pull the three bearings off the joint. Wipe the end of the joint clean so you can see the metal clip.
Now, you might have to squeeze some of the grease that's still in the boot out so it doesn't get everywhere. Put the shaft itself in a large vice, you may have to put it at an angle. Take two pairs of small pliers and grap the tabs on the end of the clip at the end of the axle, and pull OUT and DOWN. You may have to even pull one side of the clip out of it's divet, and then work the rest of the clip up and out.
With the clip off you can slide the three pronged claw thing off. Now, you can take the outer boot and slide it down the axle shaft and off. Same with the harmonic damper if need be, but spray some WD40 or PB-Blaster on the damper because it's hard to slide off. Mark where on the shaft the damper is before removal, as it's best to put it in the same spot as before.
A few notes about reassembly-
Use only CV joint grease, it's much thinner than all purpose moly grease. You really don't have to use much at all, too much is bad. Just replace some of what was lost upon disassembly. When the joints are exposed check them for wear.
You should use new ring clips on the ends of the joints.
You'll find it's kind of difficult to get the inner joint back together, just set it up in line and then wiggle the outer housing in circles. You'll get it.
As far as the boots, make sure they are under neither pressure nor vacuum when you finally set the clamps. It's best to use OEM or equivalent metal clamps, but I suppose you could use a large, very heavy duty zip tie. Make sure you get it really tight with pliers. If you need to neutralize the pressure inside the boots, use a little pick or screwdriver.
So, don't read into this guide and worry about it too much, once you take the inner boot off and expose the joint, it's all comes together.