to the OP- as mentioned it could be a number of items- lean condition/ vacuum leak, timing issue, ignition part failing, intake valve hanging open. If you dont know how to work on these cars learn, as they are 30 years old and will be costly to have someone keep fixing it for you.
@jrichker please for how to run the codes
First problem: you own a 24 year old car with some undescribed modifications and when it doesn’t run right you have to take it to a mechanic. Fox body Mustangs are hobbyist cars, if you don’t have some mechanical and diagnostic tools and skills, you bought the wrong car. The
“mechanic” will end up owning your wallet and you will hate the car; it will be a money pit and never meet your expectations. These are cars for guys who like to tinker with cars; many of the owners have been fixing cars since their late teens
If that doesn't describe you , you have my sincere apologies.
In most cases, these cars have changed hands numerous times and each previous owner did a little something to alter the car from its original state. Some of the work was excellent, but that is rare; just because it is shiny and loud doesn’t make it excellent. Some of the work was good, some of it was passable and some of it was roadkill engineering by people that shouldn’t be allowed anywhere near a car with any kind of tool.
There are numerous bit of information missing that are needed to diagnose your problem. Engine mods: heads, intake, cam, MAF, Injectors, cubic inch displacement, ignition system, fuel system, turbo or supercharger, NO2? All this information is needed so that we know where to start.
Lean condition or possible vac leak.
Step #1. Run the engine codes
Dump codes sticky
Look at the top of the 5.0 Tech forum where the sticky threads are posted. One of them is how to dump the computer codes. Codes may be present even if the CEL (Check Engine Light) isn’t on. You don’t need a code reader or scanner – all you need is a paper clip, or if your lady friend has a hair pin, that will do the job.
I highly suggest that you read it and follow the instructions to dump the codes.
http://www.stangnet.com/mustang-forums/threads/how-to-pull-codes-from-eec4.889006/