Pontiac Repair: Engine Bogs and stalls when I give it gas, twin cam engine, water in the fuel

Question
I have 2002 Pontiac SunfireGT with the 2.4L Twin cam engine.5speed manuel trans with just over 90 000KM. When I start the car when its cold it runs rough, and then runs smooth when it warms up and the Engine light flashes. If I give it gas when its in nuetral or driving, as soon as the RPMs hit 2000 it bogs really bad and has no power.The problem started when I ran out of gas. that night I drove it and it started losing power the more I drove it, until the next night I tried to go to work and It didnt have enough power to get going in 1st gear. I let it run at about 2-3000 RPM for like 10-15 min and it got better and I could drive,but I could only go about 40KM/H. I got it home the next day and took the gas tank out and cleaned it and the fuel rail and took the lines off and blew everything out and replaced the fuel filter and fuel pump cause there was quit abit of dirt (and some water) in the gas tank and gas lines. But the engine still runs the same. I checked the spark plugs and theyre still good but they were really black. When its running its like its not getting enough gas when you rev it up. The only other thing I can think of is the fuel Injectors or something with the computer or ignition module. [The dirt and water in the fuel system got there 5 months ago from driving down a flooded street in 2 1/2FT deep water, a week after that the engine lost power when accelerating and ran rough when it was hot outside but ran good and had good power when accelerating when driving at night when it was cold, and it ran like that until 3 days ago when I ran out of gas] what should I do now?

Answer
Hi, this could be any thing from the ignition module to the o2 sensor and catalytic convertre. Have a diagnosis done on the system. This will save time and money in the long run.
This is what i beleve what is wrong, the ignition coil huosing is braking down when it gets hot.