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Assuming the battery has a good charge, connections are good and the transmission neutral safety switch is good I would take a close look at the electrical portion of the ignition switch.
The tires could be a problem however I have also seen axles cause this condition. The way to tell the difference is during acceleration if the car vibrates excessively and goes away when you let off the gas I would look at the axles. Make sure the engine and transmission mounts are good.
One of the easiest ways to check the to see if the timing belt has stripped is to remove the distributor cap and see if it turns when the engine is cranked. All the basics must be in place for the engine to run. Ignition, fuel and compression(timing belt correct and working properly). These things must be happening at the right time then you can narrow down were the problem is.
Water getting into the cylinder created a slight hydro lock. This happens when excessive fluid is in the cylinder and the piston moves to Top Dead Center. The fluid cannot compress and therefore damage occurs. There could be valve train damage, lifter or bent valve stem at the top above the valve guide. Most technicians think a hydro lock damages the bottom end. In some cases it can cause damage in the valve train which is in the cylinder head on this vehicle. The only way to determine what is going on if the noise don't stop is to do a mechanical inspection which involves partial dissambly. A compression test on that cylinder would not hurt if the vehicle continues to run rough and or make noise.
You have an issue with the front caliper or brake hoses due to uneven brake pad wear from one front wheel to the other. Also if the vehicle is driven before the brakes lock up could indicate brake fluid contimination. I have seen this many times when power steering is put in the master cylinder instead of brake fluid. This happens because brake fluid and power steering fluids are available in similar containers. Not paying attention to what you are doing can cause this to happen.
The best advise I can give you is as follows. This has to be a hobby or second car. Do as much research as posible to make sure you get what it takes to pull off a sucessful modification job and finally be prepaired to spend money.
I have see this problem many times.. When you drive the vehicle at high speeds and come to a stop, the egr valve gets very hot and can stick open. A stuck open EGR valve causes the MAP sensor to get inconsistant readings and will cause the vehicle to emit black smoke and want to stall. Check and make sure the EGR valve is not staying open. Another area of concern is the Idle Air Control Valve. Because of the age of the vehicle it can stay closed some times due to carbon build up in the throttle body. One other area of concern is a lose vacuum hose going to the map sensor mounted on the back of the firewall behind the intake manifol.. If this hose is off it can make the car run rough and cause it to stall at times. The vehicle needs to be inspected by a shop who understands the varous systems at work to accurately determine the cause.
First things forst. Do not start the engine until you are sure the vehicle has the proper amount of oil. If the oil level is correct have the vehicle towed to a shop for inspection. There is internal blockage or failure.
This is a common problem on vehicles with what we call Direct Ignition System. On this particular vehicle each cylinder has a coil install directly on the spark plug. When on coil fails, the check engine light flashed for this particular condition because raw fuel is getting into the exhaust system. This vehicle has atleast two catylic convertors. Raw fuel in the system will cause the convertors to overheat and melt down internally causing more expensive problems. The flashing light is telling your that the vehicle is not safe to drive. Have is checked by a professional ASAP. Be aware this is a fire hazard.
There are still many things to be taken into consideration. Ignition spark, fuel pressure, quallity of fuel and that is just a starting point. In short, the vehicle needs to be inspected at a qualified repair shop familiar with that product. This is not something that can be solved online because there are too many variables.