That's Rich!
 

For quite a few years, I have been running the following set-up: 5.0 block (stock from Ford Racing), AFR 185 heads, 1.7 roller-rockers, E303 Cam, 24 lb/hr injectors, 70mm throttle body, GT40 upper and lower intakes. This combination has always performed very well - good mileage, great power, very smooth. However, it has also always run very rich. My exhaust pipes are quite sooty, and I can smell a lot of gas in the exhaust. I have very carefully (and repeatedly) searched for any possible exhaust leaks and not found any. I also cannot locate any vacuum leaks.

My question: Is the stock, factory computer from an '89 GT able to deal with my mods and add-ons okay, or is some sort of "flashing" required?

Any other ideas as to why I might be running rich?

Soot and smell is not an indication of rich. Unless you get a CEL indication a rich condition or you have an a/f meter monitoring the system you dont really know if its rich or not. If it were in fact very rich, you would most likely notice it in idle and or drivability.

Try pulling codes to see if any are present.The cel doesnt have to be on in order for codes to be present.A scanner is Not needed.Just use a jumper wire connected between the STI terminal and the Signal Return terminal at the self test connector,turn the key on and start counting the flashes(if present) of the cel & write down the codes flashed.
You dont by any chance have a breathered oil cap installed do you,at the valve cover?? That will cause a vacuum leak,making the engine run rich due to a lean o2 sensor reading.If the o2 reads lean the ecu will richen the fuel trim in an attempt to bring the afr back to stoich.A loose or disconnected hego ground wire will also trigger lean codes.Its the orange wire with a ring terminal thats mounted to a rear intake stud/bolt.Its part of the fuel injector harness.The egr valve,tb,iac & intake gaskets,injector orings,tab/tad solenoids,etc are other possible vacuum leak areas.The following link details possible causes of lean/rich o2 codes and conditions.
http://sbftech.com/index.php/topic,29771.0.html

BTW- is your egr system,smog system and converters still in place or have they been removed??

One last area to check,after all other possibilities have been ruled out,is the ecu.With enough age and wear,the 3 blue electrolytic capacitors on the printed circuit board will begin leaking or buldging.This will cause rich conditions.They can be inspected by removing the ecu then removing its front panel.