Are you paying this mechanic? Were you told the distributor was good?
A 2001 does not have a distributor.
A bad TPS sensor is not known to cause a 2001 to run rough. It may cause a high/rolling/eratic idle, slightly poorer throttle response, or poor WOT response.
Today's cars simply will not run right with even a tiny vacuum leak. Replace any/all vacuum lines that are soft/hard/weak/brittle/split/oil soaked. Inspect all PCV lines, oil dip stick, oil filler cap, intake lines/couplings, or any place air can enter.
This may be bad O2 sensors. But if this car has over a 100k miles, consider replacing. At the min, it will improve the fuel mileage.
Normally rough running is misfire (fuel or spark). However, it can be MAF, CKP, CAM sensor, amoung others.
Under what driving conditions is the car running rough? Idle, crusing, WOT. Does it happen all of the time, only when hot/cold? Certain speeds? Did it run rough before the CAI was installed?
There is also a Ford TSB that may apply. It deals with an incorrectly installed cam sensor.
Engine Controls - Engine Surge/Rolling Idle/DTC's Set
Article No.
02-22-1
11/11/02
^ DRIVEABILITY - SURGE/ROLLING IDLE - GEAR
DRIVEN SYNCHRONIZERS - INCORRECT
INSTALLATION - CAMSHAFT POSITION
SYNCHRONIZER (CMP) INSTALLATION TOOL
CORRECT APPLICATION
^ ENGINE - GEAR DRIVEN SYNCHRONIZERS -
INCORRECT INSTALLATION - CAMSHAFT POSITION
SYNCHRONIZER (CMP) INSTALLATION TOOL
CORRECT APPLICATION
FORD:
1994-1997 THUNDERBIRD
1995-2003 TAURUS
1996-2003 MUSTANG
1995-1997 AEROSTAR
1995-2003 RANGER, WINDSTAR
1996-2000 EXPLORER
1997-2003 E SERIES, F-150
MERCURY:
1994-1997 COUGAR
1995-2003 SABLE
1997-2000 MOUNTAINEER
ISSUE
Incorrectly installed gear driven camshaft position (CMP) sensor synchronizer assemblies may be hard to diagnose. Vehicle may exhibit poor fuel economy, driveability Diagnostic Trouble Codes (DTCs) P1336, P1309, P0340 with MIL light on. Loss of power, surge, hesitation and runs rough on acceleration may also be present.
ACTION
New diagnostics have been developed for WDS to diagnose incorrectly installed gear driven camshaft position (CMP) synchronizer assemblies. Refer to the following Service Procedure to diagnose a possible mis-installed synchronizer assembly and proper installation procedure.
SERVICE INFORMATION
Items Covered In This Article
^ "Hall" vs. "VRS" sensor function
^ Vehicle history scrutiny for past service of the synchronizer assembly
^ WDS - Power balance test
^ WDS - CMP and CKP wave signal comparison
^ Wave Comparison chart - CMP vs. CKP
^ Correct (CMP) synchronizer installation tool application & installation procedure
^ "Top Dead Center" (TDC) alignment
^ Synchronizer installation tool application chart
Hall - Effect (Hall) and Variable Reluctance (VRS) CMP Sensors
CMP sensors are used on all current model year engines, regardless of fuel system or ignition system type. The CMP sensor provides the Powertrain Control Module (PCM) with cam position information to indicate # 1 cylinder, on the compression stroke
There are two different types of CMP sensors:
^ The three-pin, Hall-effect sensor (Figure 1)
^ The two-pin Variable Reluctance sensor (Figure 1)
Although the Hall-effect (three-pin) and the Variable Reluctance (two-pin) CMP sensors perform the same function, their signal appearance is quite different and they are not interchangeable.
^ The three-pin Hall-effect sensor uses a Hall effect device and a magnet to generate a digital square wave signal (Figure 2)
^ The two-pin Variable Reluctance sensor is a magnetic transducer, which uses differential voltage across windings to generate a voltage waveform that is similar to a sine wave (Figure 2)
Both sensors provide a switching voltage as the engine rotates.