I tried almost everything suggested in this thread on mine. I spent 3 hours trying to get the phucker out. Then my cousin walked in (I was in his shop) and grabbed an air chisel out of his drawer, plugged in the air, stuck a punch in it and BPHTBPHTBPHTBPHTBPHT!!!!!!! out in one second. I guess that's what you do when you've been doing it for 13 years. If you have access to air tools, there's certain things on a motor swap that only take seconds.

Here's another idea... Take a deep welled socket that's bigger than the diameter of the dowel pin, a 8" C-clamp, and a small bolt that's a little smaller than the transmission dowel pin. Put the socket between the top of the dowel pin so that it will freely go into the socket when being removed, and place the bolt on the other end of the clamp so that it's against the dowel pin. Tighten the clamp, and it should push the dowel pin out. I didn't try that in my 3 hours of struggling, but it would have worked.

Go to Honda. Get a new dowel pin. Those aren't reusable. Your shifter will feel sloppy if you do, and it has a chance of falling out over time if you have a heavy shift hand.