My thoughts...
1. LT's are a little harder to install, but not bad.
2. If you get 94/95 LT's, then there will be an EGR bung.
3. You can get by without O2 extenders by pulling the existing O2 wires out of the looms, but extenders are easier.
4. The LT will make better torque across the entire RPM range, but it will not be all that dramatic. And with an otherwise bone stock setup, you might actually see a slight decrease in low-end torque.
5. If you live in an exceptionally cool climate, and daily drive your Mustang in the winter, you might have some issues with O2 sensor cooling. And as a result you might have some issues passing emissions. Or not.
6. LT's will sound better, and they don't drone as much as shorties.
7. Remember you'll need a new mid-pipe to match the LT's.
8. On an otherwise bone stock car, LT's would not be my first modification unless I was doing a lot of mods in a short period of time anyway.
9. Make your plans first, before buying anything at all, and then work towards that goal. You'll save money and effort by not having to re-do anything, and by having parts that work together to make the best combo.