Just a few thoughts, I by no means mean to imply this is everythiing, but pretty much everything here will need to be done.
for motor mounts look at these
http://cgi.ebay.com/ebaymotors/67-71-MUSTANG-MOTOR-MOUNTS-390%2F427%2F428%2F429CJ,-PAIR_W0QQitemZ360204620228QQcmdZViewItemQQimsxZ20091104?IMSfp=TL091104192004r11786you need heavier front springs, a larger radiator a different transmission cross member, your shock towers will make it a very tight fit. Factory cars were actually built by small custom shops and the shock towers had to be carefully massaged to get the motors to fit (beat on with sledgehammers is more like it.) Altering the shock towers can be done by cutting them and welding them back together to create more width in the engine bay, but you will possibly need to rework the front suspension mounts afterwards. the added torque will twist the crap out of the body without subframe connectors. If the rear end is an 8" instead of a 9" you will need to swap it out. If you do not have power disc front brakes, plan on an upgrade to help stop the car with the added weight and power. Larger rear drums are easier than a disc brake conversion and will do just fine. Use caution in closing the hood the first time, you may not have much clearance. (Seriously, before installing the carb, find a way to measure under hood clearance I would tape a piece of 1" styrofoam to the underside of the hood and add slats of wood over the engine to get close, one at a time until they touch, then you know how much room you have to work with)
make sure and upgrade the U joints as you will likely be building a custom driveshaft
add one piece export braces and a monte carlo bar across the engine compartment
That should get you started. If you can find a donor vehicle Torino and cougar parts work you'll save a bunch of time and money.
I love the idea of a 429 in a Mustang and considered it in my 73 351 Mach 1 (which is an easier swap due to the larger engine bay, common radiator, and 9" rear end) but the extra weight and cost associated with it was more than i was comfortable with (not that spending $2500 to upgrade heads and cam was all that pleasant, but it was managable)
Unless the 429 is built, a nice 351C with just a few upgrades will make comparable power without much of a weigh penalty.
For that matter a Boss 302 clone would be the shit in that car!