Engine surges, runs rough upon starting and while idling. Had trouble with door locks not working and the malfunction light was on at times. Engine was running very poorly. We looked on net and found that taking the neg bat cable off helped some so we tried that and has fixed the door locks and the malfunction light has turned off but engine still surges while idling. Engine is running better than before at higher speeds.

Clean Throttle Body (both sides, not just what you can see) and MAF (mass air flow sensor) [spray and shake to dry].

https://www.google.com/search?q=2001+Ford+Focus.+running+rough+and+power+surges
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Jimoh, RE POST your question with more detail.
Year, make, model, engine size,etc.,is the engine light on, are there any codes, was there any recent work done on vehicle.

press the helpful button

The EGR valve opens when the engine is warming up, which allows exhaust to enter the intake manifold. This is essentially "extra air" coming into the engine. The engine has an "idle speed control" function, which is either a solenoid or small stepper motor connected to a valve that allows a controlled amount of air to "sneak" by the throttle plate in the throttle body. Fundamentally, it is the amount of air entering a fuel injected engine that controls engine RPM. A defective idle speed control ("ISC) motor or solenoid can cause the problem you stated. (I do not know which type is used in your BMW.) Often, a check engine light will illuminate of the engine computer cannot adequately regualte engine idle speed.

What are the trouble codes in the engine computer ?

Have you checked the computer for trouble codes yet ?

The engine in your car is designed to run smoothly with maximum power output and produce as minimal emissions as possible. When your car's engine is not performing properly it can cause, low gas mileage, low power output, increased emissions and possible internal engine damage if left untreated. This troubleshooting guide is designed to isolate the malfunctioning cylinder and troubleshoot to repair the problem. Before we start we need to know one of two things; is the engine running poorly at idle only and seems to be ok under power? Or does the engine run fine and it's just the engine idle condition that is the problem. If your engine is idling rough please visit, engine misfires at idle If your engine cranks over but won't start visit engine wont start. If your engine won't crank over visit engine wont crank over. If your engine is running rough all of the time or intermittently you are in the right place. Below we have created a guide to aid diagnoses and repair procedure for most common rough engine running problems.

• Step 1: Anytime you have a problem with electronically controlled components such as an engine, transmission, ABS brake, or SRS (supplemental restraint system, air bag) inspect all fuses in the under hood power distribution center and under dash fuse panels using a test light. If all fuses test ok continue to the next step.
  
• Step 2: To check for problems with electronically controlled components such as an engine, transmission, ABS brake, or SRS (supplemental restraint system) and the fuses test ok a trouble code scan is needed to identify any system trouble. Use a simple scanner tool to retrieve trouble codes and check if they relate to the specific problem, like an ignition coil failure code. If a trouble code is present but does not pertain to the immediate problem like an EVAP code ignore it until a later time, after the engine is running properly. The reason we repair non-related codes after the engine is running properly is because sometime false codes can be triggered by a rough running engine. Once the engine is running properly the code present might cycle and turn itself off. You might say "if the engine isn't running right shouldn't it have a check engine light and a trouble code?" Sometimes conditions occur that will not be detected by the computer, example: if the intake or exhaust valve operation fails the computer cannot detect the failure because the problem is not sensor related, so the engine doesn't run smooth and the computer thinks everything is ok with no codes. If the trouble code retrieved relates to a cylinder misfire like an injector driver or ignition coil failure first repair these problems then re-test system. If no trouble codes are present proceed to the next step.
  

The engine in your car is designed to run smoothly with maximum power output and produce as minimal emissions as possible. When your car's engine is not performing properly it can cause, low gas mileage, low power output, increased emissions and possible internal engine damage if left untreated. This troubleshooting guide is designed to isolate the malfunctioning cylinder and troubleshoot to repair the problem. Before we start we need to know one of two things; is the engine running poorly at idle only and seems to be ok under power? Or does the engine run fine and it's just the engine idle condition that is the problem. If your engine is idling rough please visit, engine misfires at idle If your engine cranks over but won't start visit engine wont start. If your engine won't crank over visit engine wont crank over. If your engine is running rough all of the time or intermittently you are in the right place. Below we have created a guide to aid diagnoses and repair procedure for most common rough engine running problems.
Car Repair Guide - READ COMPLETELY BEFORE BEGINNING

• Step 1: Anytime you have a problem with electronically controlled components such as an engine, transmission, ABS brake, or SRS (supplemental restraint system, air bag) inspect all fuses in the under hood power distribution center and under dash fuse panels using a test light. If all fuses test ok continue to the next step.
  
• Step 2: To check for problems with electronically controlled components such as an engine, transmission, ABS brake, or SRS (supplemental restraint system) and the fuses test ok a trouble code scan is needed to identify any system trouble. Use a simple scanner tool to retrieve trouble codes and check if they relate to the specific problem, like an ignition coil failure code. If a trouble code is present but does not pertain to the immediate problem like an EVAP code ignore it until a later time, after the engine is running properly. The reason we repair non-related codes after the engine is running properly is because sometime false codes can be triggered by a rough running engine. Once the engine is running properly the code present might cycle and turn itself off. You might say "if the engine isn't running right shouldn't it have a check engine light and a trouble code?" Sometimes conditions occur that will not be detected by the computer, example: if the intake or exhaust valve operation fails the computer cannot detect the failure because the problem is not sensor related, so the engine doesn't run smooth and the computer thinks everything is ok with no codes. If the trouble code retrieved relates to a cylinder misfire like an injector driver or ignition coil failure first repair these problems then re-test system. If no trouble codes are present proceed to the next step.
  
• Step 3: The spark plugs in your engine are used to ignite the compressed fuel air mixture. If the condition of the spark plugs are fouled by excessive fuel or carbon the engine will not start, backfire or run rough. Remove all spark plugs to inspect the condition of the plug. Please use this spark plug condition reference guide to see how the spark plugs are operating.
  
• Step 4: Check for broken or dilapidated vacuum hoses on and around the engine, your car's engine is designed to run on a system that can hold vacuum. Vacuum hoses are typically connected to the engine intake manifold and will supply engine vacuum to various accessories like power brakes. Some cars are designed with a larger vacuum transfer hose like Ford that connects the intake manifold to the IAC (idle air control) motor. A broken or dilapidated vacuum line or air intake boot can cause the engine to lose vacuum which will allow the engine to run rough and die. Inspect all engine and accessory vacuum lines to look for missing, torn or dilapidated lines and replace as needed. Also have a helper rest their foot on the gas pedal just enough to keep the engine running. Check the engine when it is running to listen for any whistling noise coming from the engine that is not usually present. Follow the noise and inspect vacuum lines in that area. Also, when the engine is running it will pull inward a broken or weak piece of the hose to create a larger vacuum leak. Check the integrity of all vacuum hoses at each end of the hose. Typically this is where a vacuum hose fails. If all vacuum hoses check "ok" proceed to the next step.
  

Also check here: http://www.2carpros.com/articles/engine-misfires-or-runs-rough

Is your "check engine" or "service engine soon" light on? Lacking power is usually an emission system problem, for instance possibly a bad EGR valve or mass air flow senser. O2 sensers are common to fault but normally doesn't cause power loss usually causes alittle rough idle. Could even be a pluged catalic converter to. have the truck plugged into a scanner, that will tell you the trouble codes and fault info.

It sounds like the timing belt is off a tooth. Did you have it scanned to see what code was in the computer? These engines will surge when the cam timing is off.

I would not recommend just resetting the light unless you have corrected the reason it was on…..Your vehicle’s computer system has self-testing capability. When the computer senses that there is a problem with one of the components or sensors it stores the correspondent trouble code(s) in its memory and lights up the "Check Engine" or "Service Engine Soon" light to tell you that there is a problem and you need to diagnosed and repaired it. The list of possible codes number in the hundreds. The code itself doesn't tell exactly what component is defective - it only indicates where to look, or what engine parameter is out of normal range. You or a technician will have to perform further testing to pinpoint cause and the proper repair. Even if you reset the light, if the underlying problem is not addressed it will come back on. I have seen the computer make the fan run all the time when it sees a problem with the coolant temp sensor.