damn that is a beast of a motor. 8.6 liter? wow. and on a side note of what the guy said about 1000hp. sir that is an understatement lol everything in that engine is forged and ready for 30psi of boost, which in deffinently would in theory triple your hp. i would hope this is a drag car cuz this car will be illegal in no time. i'm honestly not sure if you can put that motor on the frame, mustang does put the motor right on the frame unlike other cars with f platforms but i think you would have to reinforce the frame.
your going from a 400lb v6 to a 750lb super v8. think of it this way. yer 4.0 v6 is 242CID, that means roughly each cylinder is 40.3CID since this is a v8 your putting in you add two cylinders to this equation, 521CID has each cylinder around 65.2CID, so in short yes the motor will fit width wise, and since the mustang is suppose to house a v8 it should fit length wise as well.
i'm not sure why you want so much hp tho. if you do this and put on that boost like the motor is intended to have you'll have the fastest mustang ever built i promise lol this car would be legendary but you might wanna get an open diff as well cuz one wheel burnouts with that power just isnt gonna fly.
if i were you, i'd sell that v6 and buy a v8 cuz there suspension, layout, ect. is so much better plus you already have lsd's not to mention all the wiring would already be there. you'd basically swap out the motor and tranny like you said with no other bull crap that you'll have to do swapping a v6.
you can ask anyone on here, i was gonna swap a v8 into mine and they gave me loads of commentary on stuff i'd need to do. lol
but this is my two cents so good luck man. if you keep the v6 i hope spending that much is worth it.