Let me make sure I'm understanding you correctly. Are you having trouble getting the axle to snap into the transmission, or are you having trouble getting it to go through the hub where the brake rotor is? If you didn't have the axle clipped into the trans and started it up and the axle popped out and the splines started rubbing it's possible you damaged the splines, but if you shut it down right away you shouldn't have damaged it that bad. Check the clip on the end of the axle and make sure it's not bent or opened to wide. You just need to use some force sometimes to get that axle in. Have someone pull the wheel bearing and hub out of the way and grab the end of the axle and force it in like you are plunging a toilet. Once it clips in you'll feel it. Don't be afraid to use some force. If you are nervous just get a new axle clip from the dealer it shouldn't be more than a couple bucks.