the explorer motor is almost the exact same as the 93-95 cobra, with the exception of the cam, upper intake (use it), valve springs, and timing, oil, and valve covers (and some of the related parts, you'll see if you get it). the explorer cam is TINY and tuned for low rpm torque, even the stock mustang cam is better, a lot of the gt40/p/explorer guys go with something like the tfs1, b-cam, or something in that range, and any of them require a spring kit (~$100-150 new for the tfs kit, fairly simple to install). only thing you have to watch out for is if its a p-headed motor. not a big deal if it is (they actually make a touch more power), but make sure you have the right headers otherwise plugs and wires are going to be a bitch (ask how i know........).
the hyper pistons wont really be a problem on a n/a or low boost setup, same as the 93-95 mustang ones (supposedly they're about .020" deeper in the hole, not a deal breaker, gives you a bit more valve clearance).
if you have the stock mustang motor still, take the timing cover, fuel rails, and distributor (the explorer uses a distibutor-less ignition) from it, and it'll drop right in.
now whether its worth it or not depends on what kind of shape your stock motors in and what youre future plans are. if you do go the explorer route, be aware that theres going to be probably another $200-300 or more worth of stuff that needs to go with it (cam if youre not using the mustang one, springs which you'll need either way, other odds and ends that go with a motor swap). if youre stock motor doesnt have a ton of miles, it may be more worth it to just grab the heads and intake and be done with it, and then sell off the explorer short block with the mustang heads and intake on/with it.