I have the full prothane kit installed in mine. The keys rattle at idle but it's not intolerable compared to the other discomforts (decel growl, stiff coilovers, etc). I still have balance shafts so I'm sure the vibrations are not as bad in mine as for built motors.
Early versions of the prothane kits used an insert that worked with your factory rubber but the revised kit is a complete replacement. You have to press out the old rubber as well as the metal sleeves and then the new polyurethane slides right in. Some people argue that you should only replace a few of the mounts and leave a few of them at factory spec. Personally, I disagree. The primary load bearing mounts are the two sides. The factory mounts have built in "sag" so I wouldn't want to run one of each for these - they should either both be factory or both be poly. And since the torque on the driveshaft "can" twist the motor in the bay, I say go poly. Then there's the rear mount. Most argue that this is the one that contributes most to vibration, but it's also the main roll-stop, so I say go poly. The front mount has the easiest job, it helps with roll stop but it's attached to the cross member, which has a bit of flex through the subframe bushings, and the bushing inside the mount is oversized to allow for variations in geometry when assembling. You could get away with a factory mount here, but since this one contributes the least to vibration you aren't really saving anything. So I say, go full poly all the way around.
That being said, there are things you could do to soften those poly mounts up a bit. The big one for me is trimming. The two side mounts are way to wide as they come from prothane. The fit inside the mount cylinder just fine but you have to squeeze them to get them into the chassis mount. That defeats the purpose of the mount, which is supposed to joint the motor to the chassis through the bushing - the polyurethane should not make direct contact with the ears on the chassis mount. So, I used a really sharp knife and cut a few mm off of both sides for both mounts, incorporating a mild taper, until the polyurethane cleared the chassis brace and just barely touched both sides at the widest point, right where the bushing goes through the mount. The bushing is then squeezed between the chassis uprights when you tighten the mounting bolt, just as it should be. For the front and rear I didn't have to be as aggressive with the trimming but I still did a little if I recall correctly.
The second thing you can do is to soften the mounts up with some careful drilling. I haven't done this myself, but I probably will next time I pull the motor. I'd advocate using a 3/8" bit and putting anywhere from 4 to 10 evenly distributed holes, drilled all the way through and parallel to the axis of the center bushing. And, just because I'm super OCD about this kind of stuff, I'd use an odd number of holes just to make sure that there's no preferential direction that is stiffer than any other (there are fewer directions of symmetry with oddly distributed numbers).
