Like these guys have said, even though a 4.6 is only a 281 it's a lot wider than the old pushrod motors.
The best/easiest way to do it is to remove the strut towers completely and go to an SLA front suspension. You can buy them aftermarket or find an old Mustang II that used SLA.
After you get it set in the bay you'll have to measure for the transmission. I always go for manuals so the best route here would be to go with a T56. It's a little bulkier than a T45 or TR3650 but it's well worth it. The shifter is in the same location on all three transmissions.
Then you'd have to get your driveshaft squared away. You'd probably be able to just get the correct flange on the differential side and have it cut to length.
And finally you get the fun task of wiring it. I would think it'd be the easiest to just get a donor car and strip all the wiring out of it and use the ECU, gauges, wiring, etc. that way you'll eliminate a lot of the bugs from trying to piece something together. Unless you've wired projects like this before, then by all means go the custom wired route
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