Help! Bike won't start. No spark / Solved!

So my 2009 WR250R, which I've had almost 3 years and has about 4500 miles on it failed to start for only the 2nd time ever. First time was right when I bought it. Bad fuel pump. Bought the $60 Quantum one, swapped it out and all has been good tilll.....last weekend. I bought an EJK fuel programmer and finally removed the plunger on the airbox and sticky taped the flapper door down. I hooked up the fuel programmer but very foolishly connected the ground of the ejk to the positive terminal. When I went to start I only got a click, click click and my first error code ever which was 43. "Fuel system voltage (monitor voltage) - Supply power to the fuel injector and fuel pump is not normal" I immediately caught the error and properly connected the ground but  still only got a click when trying to start. I thought it sounded like a dead battery which it was. I hooked it back up to my trickle charger and the following night the bike at least was not making the clicking sound but trying to turn over. But will not fire up. I opened the throttle while trying to start and still nada. I pulled the spark plug and noticed there was some gas on the tip. So apparently no spark. I changed the plug while I had it out. And even installed a brand new tusk lithium battery to be safe. Same results. Does anyone have a better idea where to go from here? I'm hoping I didn't fry the ECU cause they are not cheap at all. I'm tempted to try and put everything back exactly as before cause there was NOTHING WRONG before I tried all this. But the first thing I did do was remove the fuel programmer and still had no luck. I bought a new coil pack but it won't be here for a week. It's not oem either and I hear they rarely go bad. Any thoughts? The weather is perfect here in Massachusetts and I can't ride. It's killing me but I guess at least I'm learning some new wrenching skills. Help me obi wan....you're my only hope.....

First of all, I presume that because you were able to interpret Fault Code 43, you have the service manual.

For the actual troubleshooting: Fault Code 43 will not prevent the bike from either cranking or starting, so something else must have gone wrong. If the ECU had been damaged you would be seeing Fault Codes "Er-*", so it seems the ECU is fine.

Did you measure the original ignition coil and determined it was bad?

Most crucially, did you check the fuses?

Hey thanks for the response. Yes i have the service maual on my phone. Might print this out at work rn actually. I checked with my multimeter the fuses in the box near the coolant tank and the 30amp fuse connected to the starter relay. (directly right of the battery). All were good. These are the only ones i have found so far. I have yet to measure the resistance on the coil pack or anything else yet. Will be doing that tonight. After running the diagnostic last night I noticed another fault code that was stored. Code 46. "Power supply to the ECU system relay isn't normal." I didn't see this come up initially, only code 43 but it makes sense that both may have happened together. I'm relieved that it's hopefully not gonna cost me $600 for a new ecu. I'm gonna check for spark tonight along with checking my stator and regulator/rectifier and coil pack as well as other relays. So there is an ECU relay too? Sorry but I've been learning as I go. What else am I missing?

Fault Code 46 also wouldn't prevent the bike from cranking and starting.

If you have checked the fuses, then go into Diagnostic Monitoring Code 61 and take a look at all the Fault Codes that have been posted. If 43 and 46 are the only ones there, then go into Diagnostic Monitoring Code 62 and erase the Fault Codes. Once you have done this, go to Diagnostic Monitoring Code 63 and confirm that "00" is displayed. Turn the bike off, turn it back on, and try to start it.

I actually did that last night.There were only two other codes in there. 30 and 70. One is the lean angle and the other was the bike shutting off if it's been idling over 20 minutes. Both of those must have been by the previous owner although I did drop it once offroading. I cleared them all and now have all at zero. Bike still won't start. I did pull the plug and coil pack and checked it against a grounded bolt. I DO have spark after all. I just saw gas on the plug so I assumed I didn't. I think tomorrow I'll drain the tank and check out the fuel pump. I also need to check for compression too I guess.

Good news about having spark.

You don't need to empty the tank or remove the fuel pump yet; just listen when you turn the key: does the pump prime?

Problem solved! I was about to try starter fluid and upon opening my airbox I saw this. (See attached picture). I have summised that I killed the battery when I attached the ground wire from the ejk fuel programmer to the wrong (positive) terminal. (So dumb. I know) After trying to start it numerous times I flooded the filter and the airbox. A major obstruction. After completely removing the filter and cleaning out the airbox she fired right up. The no toil split apart upon trying to clean it but my bike is running again! Anything else i may need to be aware of after that much gas sitting in the airbox for days? I pumped it all out and cleaned it with a rag. Put the oem filter back in until my new no toil filter shows up. Thanks for your help!

That is a lot of fuel! Consider yourself fortunate that you didn't hydrolock the cylinder.

The bike works, so you don't need to do anything else.

Yes that IS a lot of fuel. I'm also lucky it didn't turn into a molotov moto. I'm still trying to wrap my head around exactly how this happened. Gonna do an oil change when I get home just to be safe. Praying no fuel got into the engine itself, which it may have. I should be able to tell even just by how high the oil is in the sight glass but I'm not gonna take any chances.

Good call, with so much fuel flowing into the cylinder, some of it may have trickled down past the rings.