Yeah, you should just buy a complete swap. That way the engine will be paired with it's ideal transmission. As far as mounts go I don't believe you'll need any special mounts if we're talking about a 96-00 Civic. All the aftermarket mounts I've seen say they will work for both B and D-Series motors. You could take the opportunity to upgrade to aftermarket mounts while the motor is out, but it's not really necessary unless the stock ones are bad or you're actually going to be racing your car or building the motor for a lot of power.
By the way, are you in the US? The "SE" thing threw me off, I was thinking of the SE Accords, which only come in automatic. Come to think of it I don't think there even is a Civic SE in the States.