Truck chugs after driving through high water

[Showmodel]

Brand new member here. Hope you all can help me out. 3 days ago I drove through a flooded road. Water got higher than I expected. Maybe to the bottom of the doors or slightly higher. Was quite a long stretch I had to drive through. Took it slow after the water got high. Never splashed over the hood. Got through it fine without the motor showing any signs of issue. Never even began to stall or hesitate. Drove home about a mile or so without noticing any issues. When looking under the hood the next day, under hood and top of motor do show signs of being wet as the dirt is "streaked" from front to back.

 

Next day truck started fine and seemed to idle smoothly (or didn't notice a rough idle). However, when driving the truck seems to chug quite often. Seems to mostly happen when under load or lower rpm's. Almost feels like bumps in the road. Tach seems to bounce up and down like 1K every few seconds. Once in a while when rpm's are below 1800 or so, I hear a deep vibration that lasts around 3 seconds and then goes away. If I give it throttle it also goes away. Truck accelerates pretty good except for feeling those "bumps" like every few seconds or so. When given full throttle seems to have full power and will rev to the limit. When cruising and taking the foot off the gas truck seems to cruise fine. Motor sounds quiet. Starts fine every time and seems to idle pretty darn smooth. Doesn't seem to be missing a cylinder all the time as I would think it would be running a bit rough at idle, unless these trucks can do some amazing compensation.

 

Never had a light come on so don't know where to start. I am pretty handy so don't mind doing work or troubleshooting. Checked the oil and is dark and does not appear to have any water in it. K&N air filter is not wet and no water in the box. Truck has been driven for an hour at least twice in dry weather so should be pretty dried out by now.

 

Did a little research and put my fingers on each COP and plug wire while the truck was running. Passenger side front wire gave a very noticeable "bounce" when touching it. I could feel it pulsating with the spark. Turned truck off and removed the cable and plug. Plug was loose enough to unscrew without a wrench on the socket and extension!! Thought I found the issue, so cleaned up the plug and connections and put it back together. Grounded the plug to the motor and started it. Plug was sparking away and motor ran very rough at idle. Put the plug back in and still have the issue described above.

 

Any help you all can provide would be greatly appreciated, as the wife will kill me if my stupidity will cause a large bill at the dealer!!! Thanks in advance for any advice.

 

BTW my 09 Sierra 1500 has the 5.3 motor.

[Dnt]

Vent for the gas purge valve on the 09 is in a position to fill up with water, disconnect at tank purge valve connection and drain it plus blow it out. Put some fuel treatment in the tank and you should be OK in a few days..

[Showmodel]

I replaced the purge valve a few years ago due to some codes that led me there. The new valve does not have a vent hook up so the original vent hose is just hanging there. Do you think I still need to pull the purge tank and empty it? Thanks!!

[KARNUT]

How's it shifting? Did you get high enough to get in the transmission or rear end? Your problem could be your transmission.

[Showmodel]

At first I thought it might be shifting rough, but when I put it in manual mode and lock it in a gear the issue still occurs while cruising and varying my speed a bit. Yes, the water was probably about 1/3 the way up the doors. Almost seems electrical to me as the rpm's jump around a bit while driving.