This is a common swap I've tuned countless of them with no issues. As long as your county isn't too technical about the engine swap it will pass emissions perfectly fine. If all they do is a quick look over for emissions components present and do a plug-in obd-2 test then it will pass perfectly fine. I have yet to have one fail emissions.
As has been stated you will need a v6 k-member since it has the sbf motor mount setup making it practically bolt in. Your modular bell housing trans will not mate up to the sbf. You will need a 4r70w auto trans from the same v6 mustang you snatched the k-member from. The trans is stout so no worries about rebuilding it or anything I've pushed 600rwhp through bone stockers and never had any problems. Your cheapest option would be to get a marauder specific torque converter and you will need a new flexplate as well. Here is a reference thread with links
http://forum.efidynotuning.com/viewtopic.php?f=24&t=2562&p=32896#p32896
Verify your imbalance as a 347 could be balanced either way 50oz, 28oz or even neutral.
You will need the balancer (again check imbalance), 35 tooth reluctor, timing cover, crank trigger, cam stalk and cam sensor from a 99-01 explorer 5L. Cut the cam sensor connector off the donor vehicle as well to mate to your existing wiring.
Toss that on your 347, slap it in the car with the new flex and trans. Everything should plug right in. Take the original coil on plugs and rip the boot off the coil. Get yourself a set of ls1 plug wires and they can be snapped on the coil. You can fab up a bracket to secure the coils to the valve covers if your up to it. No reason to go coil packs.
The remaining air inlet ducting, coolant hoses, driveshaft, etc.. is all trivial.