At 8k miles, you would not normally need spark plugs. Water in the plug well from washing or riding is possible, as Fennellg mentions. Unless someone was pulling on things or moving things around aggressively when doing the flash or removing the ECU, it seems unlikely that the plug wires would have damage.
What's the last thing you did to the bike?
Have you ever checked the air filter?
Has the problem persisted thru more than one tank of gas?
Do you always get gas at the same place?
Air, Fuel, Spark. These are the three things that make our engines run. So your problem is likely related to only one of those.
I would check the air filter and make sure the vent lines to the tank are not crimped and correctly tucked into their retaining clips down low after you are done. (you need to lift the tank and remove 11 screws as I recall. One is hidden under a rubber plug in the center of the air box lid) Use a strap or bungie cord to hold the tank up while you work. You need to pull the two vent lines loose down low in front from the retaining clips so the tank can move up. Just loosen the pivot bolt at the back of the tank, no need to remove it. The other two bolts, one at each side can be accessed by removing the right lower panel and just a few of the upper bolts on the left so you can pull it out and get a wrench in there. It's not necessary to remove the entire left lower panel.
There is a drain in the air box. Check that for oil and clean it out. It has a clear cap over the drain that can be removed from the outside.
If the air filter looks fine, while you are at it would be the time to check the spark plugs. That requires removal of the air box base as well. There are some obvious bolts and a breather hose in the middle under the air box. The breather hose has a hose clamp. Long needle nose pliers work well for that. It's a little fun getting it back on later.
Pull the breather hose up a bit to help.
Answer the questions and if you feel comfortable, take a look at the air filter and plugs. It may be as simple as bad gas.