New to site need help with a 2002 mustang gt

Hello everyone thanks in advance. I recently picked up a 2002 mustang gt from a local auction. I have zero history on the vehicle and it has some issues. Here is what I do know about it after some investigation.

2002 gt 4.6l was an automatic converted to manual. Had the auto harness still on the trans.

No check engine lights at all

Speedo is off by a lot more then double. Running a stock gear most likely. Turned the wheels and counted the driveshaft rotations thinking it’s a 3:27
Its hanging the idle around 2000-2300 I can force it down on a stop or it come down and hold around 1200-1500 for a min or so.

I suspect a fuel problem because it runs good then it brakes up between 1/4 and 3/4!throttle full throttle it’s goes good most times . Then it brakes up again. Then cleans up. Motor seems great when first fired up or when it’s hitting in all 8 under a load. It’s like it’s sucking up dirt into the pump. It’s hard to hear it running too.

Bolt ons are bbk long tubes
Bbk off road x pipe to flowmateres
Cold air intake
Get delete
Under drive pulleys
New accel coil packs
New ngk spark plugs
Manual trans added
running stock 96-98 19lbs injectors
Stock throttle body and plentum
Stock mass air
New mass air sensor
New throttle body position sensor
New idle air control valve
New vacuum lines off intake
I have removed the throttle body and disassembled and cleaned
New fuel tank filler tube.

It’s obvious to me that the car has some sort of a tune for the auto to manual conversion since they retained the auto harness I’m guessing they didn’t change out the computer . Car came with no tuner. I have a new cobra svt fuel
Pump I’m installing today I think will fix the brake up but not the hung idle. Any suggestions on how to fix the idle so I can get it tunes
Any help will be greatly appreciated
 
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If this were my car I wouldn't be in a huge hurry to throw parts at the problem until I understood WHY things are acting the way they are.

Are you aware that the speedometer does have an effect on the idle? The PCM makes idle decisions based upon the car's speed.

Here's some information on HOW to trouble shoot idle/IAC problems.

Troubleshoot IAC idle problems 1996-2004

Do you know the model year that the manual transmission? Why does that matter? Because many people assume that all transmission are interchangeable just because they look the same and bolt up. The speedometer off by double is a symptom where a transmission with a VSS sensor has been "forced" into an application is expecting an OSS sensor.

Do you have an ODB2 scanner? How could an ODB2 scanner be used to possibly save you a ton of parts and grief? Consider that IF there's a fuel related problem this will also show up in the Long term fuel trims (LTFT) and Short term fuel trims (STFT). It should be expected to see the fuel pressure (FRPS) drop off IF the fuel pump isn't able to keep up.

Here's is some information on an affordable Windows based unit.

ForScan ODB2 scanner w ELM327 USB

With an ODB2 scanner this will also give easy access to PID's such as TPMODE, IAC duty percent, LTFT, and MAF flow. Information that is super helpful trouble shooting drivability problems.