The last 2 times that I have pulled a honda/acrua engine, is I just disconnected everything except for the bitch pin, then when just pulled the engine with the linkage on. It fits. You may have to lift the engine a little higher or swing the engine off to the side of your engine bay but it will come out. Then pound it out when it is on the hoist. Much easier since you have the engine out.
As for replacing it (once you put your other engine in) Connect the other 3 spots where it bolts up, then put the joint section on the shift fork. This way, your not fighting the linkage to stay in one place. The hardest part of putting it back in is getting it started. Once you start it, it goes in fairly easily.
Hope that helped