Is there a secret trick for installing axle shafts?

Yup- sounds like your splines got misaligned when the axles were out. Some times you can use the lever approach to get them lined up. Sometimes they just wont move and you gotta take them apart and re-align the splines. I am in the same boat... and mine will not budge.

Something else just occurred to me. If you got axles with the green bearings, you might need to remove the thrust block in the clutch style sure grips. The axles no longer use each other to set the end play, and it is possible that block is preventing full engagement. But you mentioned that your old axles didn't seat anymore so it is most likely the splines.