So my son decided to tackle swapping out the blown auto tranny on our Forester with a junkyard pull and is having an issue getting the new tranny installed. He says it wont slip all the way up into place to bolt back on. Did he overlook something pulling out the old tranny or is there a trick to getting it back in place ?

Automatics are usually pretty simple. Usually if they don't pop right together it's because the torque converter isn't seated all the way in the transmission. If it gets forced together it will damage the transmission pump and the trans will be useless.

Make sure the torque converter is seated properly.