How can I troubleshoot my fuel injection system I had to replace my fuel pump. And filter and clean water and rust out of the tank .will a. Clogged injector cause it to miss on two of the cylinders and how can it be fixed

If fuel pump is new you should have good pressure before injectors, but check pressure anyway. If pressure is low go back and check for a bad fuel filter between tank and engine and replace. Fuel lines get clogged because of moisture in the lines causing rust. Did you replace the under pump fuel filter? Back to front, if pressure is good , injectors may be the problem. Do a compression test to see if your engine is starting to die. I have only given you an idea of what to look for. You will either have to check yourself ,or have your truck checked by a shop. GOOD LUCK FREIND.

Did you replace the fuel filter? Sounds like it is clogged.

Clean the injectors.

hole in tank
clogged filter
gas tank empty
clogged fuel line
wrong tank selected
hole in fuel line
tank clogged with rust

NO, the relay will either work or it won't. (Unplug it and look at it; if the terminals look corroded... replace it.) Most cars have fuel injection systems these days. In addition to the fuel pump that pumps fuel out of the gas tank... there is an injection system pump which is quite expensive. In order of operation: 1) have your injectors cleaned or replaced as needed (new ones run about $30 each), 2) have the injection system pump pressure checked and get a rebuilt pump if needed (brand new one ~$850), and 3) check the fuel pump. If the car has more than 80K miles on it, then suspect clogged or partially obstructed injectors. A BOSCH SERVICE CENTER has a machine to test and clean most makes of injectors. At the same time, replace your fuel filter and use good gas when you fill up. NEVER fill up from a station that just had a fuel truck delivery (if you see the tank truck) as the garbage on the bottom of the tank takes a day or so to settle back down again. Magneti Marelli Check Star also offers good injection system servicing. The dealership should be your last resort as they just replace parts until the problem goes away... leaving you with a hefty bill and a bag of old parts

It could be that you have picked up a batch of dirty fuel, or there is some dirt or rust inside the tank, that has clogged the fuel filter that is in the engine bay. Try replacing this filter first. If that only improves things slightly, it could also be that the dirt / rust in the fuel tank has clogged the gauze input filter that is part of the fuel pump inside the fuel tank.

To clean the tank filter, you will need to remove the pump assembly from the tank. Access to it is usually through a removable plate in the floor in the rear of the vehicle. Disconnect the wiring plug and the fuel hoses, noting which hose goes to which pipe and undo the screws holding the unit in the top of the tank. You may have to juggle it a bit to get it out. Once you have the pump assembly out, allow the gauze filter to dry. You can assess the amount of clogging by shining a torch through the gauze and see how much light comes through. Clean it by brushing with an old tooth brush and blowing clean with compressed air. If there is a lot of dirt/rust in the tank, try draining it. Replacing is the reverse procedure. You may have to repeat the above cleaning process in a few months if the symptoms appear again.

Check fuel pressure at rail,pump may be going,also check regulator

Check TPS Voltages

Injector Cleaner- money better spent at Dunkin Donuts

Check out EGR Valve and tube may be rusted out

It could be that in the process of having the fuel tank straps fitted some dirt or rust inside the tank has come loose and clogged the gauze input filter that is part of the fuel pump inside the fuel tank. You will need to remove the pump assembly from the tank. Access to it is usually through a removable plate in the floor under the back seat. Once you have the pump assembly out allow the gauze filter to dry. You can assess the amount of clogging by sining a torch through the gauze and see how much light comes through. Clean it by brushing with an old tooth brush and blowing clean with compressed air. If there is a lot f dirt/rust in the tank, try draining it. You may have to repeat the cleaning process again in few months if the symptoms appear again

Quick explanation of your fuel system:

An automotive fuel system consists of everything between the fuel tank and the carburetor or fuel injection unit. This includes the tank itself, all the lines, one or more fuel filters, a fuel pump (mechanical, electric, or both), and the carburetor or fuel injection unit.
With the exception of the carburetor or fuel injection unit, the fuel system is quite simple in operation. Fuel is drawn or pumped from the tank through the fuel line by the fuel pump, which forces it through the fuel filter, and from there to the carburetor/injection unit where it is distributed to the cylinders.

So with that info...try first to clean your spark plugs.
Next, replace your fuel filter.
After that, depending on a carburetor/fuel injection, try an additive that cleans the injectors. For the carburetor, try a half of can of what is called "Seafoam". It comes in a metal can available everywhere, including Walmart. It is worth the $6-8 and also will "dry" out your fuel from water. Very good product.

After that, get back to us and let us know how your Toyota is running.

A fuel filter is a filter in the fuel line that screens out dirt and rust particles from the fuel. They are normally made into cartridges containing a filter paper. They are found in most internal combustion engines.
Fuel filters serve a vital function in today's modern, tight-tolerance engine fuel systems. Unfiltered fuel may contain several kinds of contamination, for example paint chips and dirt that has been knocked into the tank while filling, or rust caused by moisture in a steel tank. If these substances are not removed before the fuel enters the system, they will cause rapid wear and failure of the fuel pump and injectors, due to the abrasive action of the particles on the high-precision components used in modern injection systems. Fuel filters also improve performance, as the fewer contaminants present in the fuel, the more efficiently it can be burnt.
Fuel filters need to be maintained at regular intervals. This is usually a case of simply disconnecting the filter from the fuel line and replacing it with a new one, although some specially designed filters can be cleaned and reused many times. If a filter is not replaced regularly it may become clogged with contaminants and cause a restriction in the fuel flow, causing an appreciable drop in engine performance as the engine struggles to draw enough fuel to continue running normally.
Some filters, especially found on diesel engines, are of a bowl-like design which collect water in the bottom (as water is more dense than diesel). The water can then be drained off by opening a valve in the bottom of the bowl and letting it run out, until the bowl contains only diesel. Many Fuel Filters contain a water sensor to signal to the ECU or directly to the driver (lamp on dashboard) if the water reach the warning level. It is especially undesirable for water to be drawn into a diesel engine fuel system, as the system relies on the diesel for lubrication of the moving parts, and if water gets into a moving part which requires constant lubrication (for example an injector valve), it will quickly cause overheating and unnecessary wear. This type of filter may also include a sensor, which will alert the operator when the filter needs to be drained. In the diesel fuel filter there is (usually) a fuel heater to avoid the paraffin (in case of lower temperature) inside the filtrating element which can stop the fuel flow to the engine.