I find having the transmission in gear helps to line up the splines as well as I run the axle through to help aid this task. Also leaving the 4 bolts on the pumpkin loose helps. They need to be loose anyway and tightened at the end.
After trying to get my back wheel on for 40 minutes, I finally consulted the VRCC forum and came across this gem. The trouble I had was the three new orings (I got the red ones) were super tight preventing the wheel from pushing all the way home on the splines. In the end I had to use a tire iron on its side between the LHS swing arm and axle spacer to very gently pry the wheel the last 3 or 4mm home.
Pushing the axle all the way thru certainly helped with the alignment.