The axles will spline up easy. Its just the last 1" that is the tough part. That's when you're trying to seat that snap ring. The first 3" or so that you slide it in, that's the splines meshing. The tough part is the snap ring groove at the end.
Doesn't pounding it in like you say damage the splines that are trying to mesh with the splines on the transmission input? However I have been just pushing and waiting. I didn't know how fragile the axles might be so I didn't want to just ram it in. I'm going to have to try this ramming procedure. I haven't tried that yet. I just get it in as far as I can go and attempt to push in from that spot which doesn't work.
The clip is supposed to look warped. its not perfectly round. Grab the outer end of the axle and push in on it. The CV joints slide in and out to allow for length changes during suspension articulation and steering. Now, slide the axle into the transmission and do the same thing but do it like you're angry. Pound it in using that compression. Don't just push and wait, pound it. Slam those puppies home. If you're not afraid of knocking the car off the jackstands, you're not doing it hard enough
Don't take the boot off... there is no reason for it, and its a mess. Its full of a thin grease that is the consistency of sour cream.
You can't remove it. The CV joints have enough compression space that they can float in and out without that clip. At the very least it will cause massive leaking at the axle seals. At the worst, the axle will come out of the transmission and cause major damage.
The axle should slide in easily to a point. Some let the ring snap in easily, others are a pain. The best way to do it is to apply your pressure or impacts with the axle straight - not angled. If the axle is angled up, then you're forcing the ring against the bottom of the hole.
Two ways that always seem to work for me. On easy axles, I grab the splined hub end of the axle and ram it in compressing the CV joints until they hammer the axle into place. If that doesn't work I use a long extension and a hammer. Put the extension on the inner CV joint and give it a good whack. Sometimes it also helps if you try pushing it in by the inner joint. A straight insertion often works easily.
The point of the axle clips is to prevent the axle from "walking" out. As the suspension travels up and down, the length of the axle changes. The point of the clip is to hold the inner joint in place during that travel. Theoretically, if it weren't there, the inner axle could get pulled out during extreme articulation. The clip gently holds the inner joint in place so it can't move.