problems with my 2006 Toyota tundra what is wrong?

Usually when you have too many codes show up on a scan it's not all of those sensors, it's the ECM. You have replaced many things connected to the ECM to I'd lean toward the ECM being the problem. Especially if you can't pull any codes from the ECM to indicate the specific sensor or cylinders affected and so on. 

Sometimes the camshaft or crankshaft position sensors go bad. BUT, I still think you need to give the ECM some consideration. Have the guys at Auto Zone or your favorite parts shop plug their code reader into the ECM plug under the dashboard and you'll soon know the answer. 

Good Luck!

You used all your guesses and wasted a barrel of money and time. Pull the OBD2 codes and have an answer that is NOT a guess. The check engine light means *check the engine* and you do that with a code scanner.

It is time to get a scanner and read the trouble codes before you lose your mind and savings.  You are just firing the "parts cannon", not the best way to fix cars.

Tell us the trouble codes after you read them. 

Typically, a flashing check engine light indicates a misfire, which is consistent with the rough idle.  There are any number of reasons why that may be, and as it stands, you are throwing parts at the problem, which will be expensive in short order.  If it were me, I would see if I could get my hands on a scan tool and check the codes to see if it is isolated to a particular cylinder.  If it is, I would check compression to get an idea of the engine's health in that cylinder, as well as check the fuel injector's function on that cylinder.  If the misfire is random, then I would check fuel trims.  Fuel trims should be around 0%, plus or minus 5%.  Take long and short fuel trim and combine, so if you long is -5 and your short is +5, that adds to 0, which is good.  If your long is -20, and your short is -20, that adds to -40, which is really bad.  Fuel trims are important because the engine needs to use a certain amount of fuel when it takes in a certain amount of air.  It must maintain that balance.  When it's not misfiring, fuel trims that are off can be indicative of un-metered air.  Un-metered air is air that is introduced to the engine without having been measured by sensors.  If the engine is taking in air that the management doesn't know about, it can't maintain the Air/Fuel balance (also called the air/fuel ratio).  If the fuel trims are off, and you suspect un-metered air, start checking for leaks from the air filter down to the engine itself.  Check for cracks in the intake plumbing, check for loose, cracked, or broken vacuum hoses, check the EGR gasket and plumbing, throttle body gasket, etc...  You may need to see a shop who has a smoke machine who can push smoke into the intake and see where it leaks from.  If you are good at fabricating, there are videos on youtube of people who have crafted their own smoke machines at home with scrap materials.  If these tests do not result in a definitive answer, I would probably consider the services of a pro

i would let a mechanic check it out

i would get a mechanic to fix it

You need the problem code.