If the tranny oil wasn't changed with the swap (which doesn't make much sense, but you never know) change it first. Stop by your local Honda dealership and grab 3 bottles of Honda MTF fluid. It's about $5 a bottle but it's good stuff. B-series trannies take 2.2 or 2.3 bottles, I can't remember which. Just fill the upper hole till it starts to pour back out and a funnel with a tube attached is very useful. I'd also bleed/change the clutch fluid (it's just standard DOT3 brake fluid, watch you don't get any on your paint) to make sure there's no air. Hopefully that will loosen it up.