You really need to check for codes as mentioned above:
@Noobz347 - The code dump procedure isn't in the sticky - you may want to add it... Dump the codes: Codes may be present even if the Check Engine Light (CEL) isn't on. Dumping the computer diagnostic codes on 86-95 Mustangs Revised 26-July-2011. Added need to make sure the clutch is...
stangnet.com
Does it just not go past 3,000 rpm? Can you slowly press the gas pedal and the rpm's go up or will it just not go past 3,000 rpm?
When checking the fuel pressure you need to set it to 39 psig with the vacuum line disconnected from the fuel pressure regulator (FPR) and the vacuum line plugged. When you reconnect the vaccum line to the FPR the pressure will drop as this is normal. When the rpms go up the fuel pressure will rise but will not go past 39 psig. If the fuel pressure does not rise then you have a fuel issue.
You replaced the fuel filter but how old are the air filter, cap, rotor, plug wires, and plugs? These need to be inspected and if needed replaced. Do not buy into the whole platinum spark plug thing with these cars. Just run a Motorcraft 3924 and they work very well. I would get a Motorcraft cap (part number DH411B), rotor (part number DR374B), and 8mm stock plug wires (part number WR4017C). If the car still has the factory air box then the part number for the Motorcraft air filter is FA1042. You can get all of this at
www.rockauto.com for a decent price but some local auto parts stores may carry them or can get them in a day or two.
If you want to get the 9mm Ford Performance plug wires (most of us run these) the part number on the plug wires will vary due to color of the plug wire:
Black - M-12259-M301
Red - M-12259-R301
Blue - M-12259-C301
So a general tune up on these cars is air filter, fuel filter, cap, rotor, plug wires, and plugs. You may need to do a base idle reset which should be covered in the thread the General posted.
Again, first thing you need to do is
check for codes.