I had a 5.0 for years...I'm sure you know this, but make sure you have a plan. What are you going to use the car for, racing or street? How much money do you want to spend? You really could go crazy, and spend a lot of money on parts that don't make a whole lot of difference. Before you do anything make sure the car's cooling system is in order, t-stat, radiator, hoses, fan clutch etc (these cars tend to run hot). Run through the fuel system; fuel filter, inspect lines etc. Then I would do Gears (3.73s is what most do for 5spd, 4.10s for autos). When you do the gears make sure the differential is in working order, switch to a trac lok if you can. Then I would do a MAF conversion http://shop.fiveologyracing.com/Mustang-Mass-Air-Conversion_c8.htm. Taking into consideration the calibration of the sensor vs the fuel injectors you are planning on using. Then I would do an H/C/I swap http://www.latemodelrestoration.com/item/LRS-6049C-K/1987-93-Mustang-50L-Top-End-Engine-Kit . http://www.mustang50magazine.com/techarticles/m5lp_0604_1988_ford_mustang_heads_cam_intake/viewall.html
You can run a blower or switch to a bigger engine, but at some point you will need to switch to MAF (unless you want to go carbureted) and address the heads and cam, so I would do this stuff first.