I'm happy to hear that you are putting a SOUL into your Mustang. I have a 1969 Mustang Mach 1 Fast Back, 4 speed car, 351 Windsor equipped, that I am trying to finish at the moment. I'm not LS swapping it, so I'm having a tough time. Keep in mind-that according to Ford enthusiasts-if you cut up the shock towers it supposedly destroys the value of the car. I don't know this to be true-but when I mentioned cutting up the shock towers to my local Ford Restoration shop he told me not to do it. My car is all original, so I'm pretty much stuck with keeping it all Ford (which makes me want to vomit). I would think that an LS would drop right in and not have any clearance issues----except with the steering box! Keep in mind the steering box is between the shock tower and the firewall on the drivers side as you probably already know... My problem is I got my car with the engine OUT of the car, and no exhaust... Now I've got the engine built, and installed, but I CANNOT find an exhaust system that will work in the car... I've tried 4 different sets of headers and ALL of them make contact with the drivers side shock tower, and also with the steering box. I'm left with ONE option.... buying an $815 set of long tube headers from Summit racing..................... I would personally rather URINATE on the drivers seat and sell the car as is before spending that kind of dough on a set of headers that will work... Honestly that's how disgusted I am with working on this Ford. If I knew then what I know now, I too would have LS swapped it, and been done by now.. Anyway, I digress...
I wish I could be of more assistance to you in your quest for information. Based on the amount of space in the engine bay, I'd say maybe think about moving the engine over to the passenger side of the bay at least 1-2".. The clearance issues I'm having are ALL on the drivers side between the shock tower and the steering box. You may have to move the trans mount location on the trans cross member a little bit as well. From the factory my engine sits CLOSER to the drivers side shock tower, and even the back of the trans is aimed more towards the drivers side of the rear of the car-probably due to the off set pinion yoke on the rear diff. I despise Fords for crap just like this. I only bought this car because it was from an estate sale and I figured I could flip it pretty quickly if I reassembled it and got it running... Regret is the word of the day... Lots and lots of regret. This is my FIRST time ever owning a ghetto-shiz-box known as Ford, and will be my LAST...
Good luck on your swap and if you move forward with the engine install-post up some pics! I'm sure the Ford fanatics will hate you for what you are doing-but F them... I LOVE your idea and wish you the best in your endeavor.