Does a noisy cad converter cause engine to run rough at idle only? I changed the plugs, removed the fuel inj. and cleaned them. I replaced the water pump so the timing could be off but I clamped the overhead cam gears so they would not move out of place when I did the water pump work. So now, it runs rough at a light but runs fine at driving speeds. It starts good cold but drive around and shut off a few minutes then start again, It then becomes very hard to start. The engine is not hot running but will get hot just idling a few minutes. This is a 1999 Ply. voyager four cylinder. Want to buy it?

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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If it is not firing on one cylinder, check and eventually replace distributor rotor, or electronic injection module.
Check also for camshaft problems.

If it is idling like it was before the inj were replaced then you have fixed the wrong problem the ethonol doesn't damage injectors you probably have a spark plug wire that is bad or a coilpack is bad or you have a fouled spark plug? A compression test can tell you of any problems with the valves! The injectors are designed to be compatible with flamible liquids ie gasoline or alcohol! I have been a mechanic for 23 years and have never seen inj fail due to alcohol in today's gasolines! You might have been scammed? Anytime you have repairs done request your old parts to be returned to you! You might have to take the mechanic who claimed he replaced your inj to small claims court! Try replacing the plug wires and the spark plugs first if no change then get carburetor cleaner and with the engine running spray the inside of the throttle body where it is black with the throttle open and engine rpms increased if that doesn't change it the coil packs might be going bad there are three so buy all three as a set so you don't have to change them at different intervals! Depending on mileage the timing belt is reccommended to be changed at 150,000 miles the spark plugs are due at 100,000 the coil packs should last over 200,000 miles so I'm guessing it is time for major preventative maintenance? The timing belt being worn can cause rough idle too!

if the car is loud/noisy there is a hole in the exhaust system and this will cause a rough idle because of a loss of back pressure and the vales will not open and close properly resulting in the rough idle it also will make the engine run hotter and this will cause your spark plug gaps to increase and the spark will be less than needed to ignite the fuel in the cylinder for proper combustion which will result in poor gas mileage and lack of power is the check engine light on?

Sounds like a dead coil pack and needs replaced cause you're getting no fire to those plugs and causing a rough idle. Another thing is, that catalytic converter will only turn red because it's plugged up and needs replaced. Have that checked out friend.

ck for leak at intake. if no leak pcm/ecm may be sending fire command to slow to # 1 . the fuel injector is always hot the ecm sends a ground to the injector. even new parts can be bad ck inj, with ohm meter resistance should be the same between each inj. im not sure of the specifications but they should read the same my jimmy specs are 1.9-2.1 any other reading is bad . no resistance or lower or higher readings my injector would be bad. 140 is good reading, timing can be off a little and still run but rough like a miss. a code wont set most misfires will set a dtc or flash the engine light to let you know damage to cat system is happening , to much fuel a system rich,to little a lean. a bad mass airflow meter can also cause a misfiring or rough idle ck with scanner if dirty clean with brake cleaner first before replacing . hope this helps some let me know how it goes.

Any vacuum leaks? Timing good? egr and o2 sensors good?

ROUGH IDLING CAN BE CAUSE BY MANY THINGS.I AM LOOKING AT LEAKING VACUUM HOSES OR INTAKE MANIFOLD GASKET LEAK.DIRTY FUEL INJECTORS AND WORN ENGINE VALVES WILL CAUSE ROUGH IDLING.ALSO LOW IDLE SPEED CAUSE ENGINE TO RUN ROUGH.

Sometimes a rough idle like that is a fuel filter. As you've already done the plugs and wires the fuel filter would be my next bet.

Your cat should last quite a while now it is replaced. I recommend testing coil packs and module. Change plugs and wires and double check your vacuum hoses.