About 6 months ago I bought a 2002 F4i and it has been amazing to me since then to about a week ago, when I lost my rear axle nut and had to let it sit in my shed until the new one got here. I got the new one today and went to fire it up, heard the glorious whine of the fuel pump, hit the ignition button and... nothing. I heard the sound of it trying to start, sometimes at least, and it actually did fire up once, but it idled around 2k RPMs and died when I let go of the gas. I gave my stepdad (former bike mechanic) a call and he told me that the battery was probably too weak to run the injectors, so I set it on a charger for 30 mins on 12V 6A and for about two - two and a half hours on 12V 2A. I put the battery back in and it and it still doesn't run, although the starter does fire every time now. Most of the time it doesn't catch at all but occasionally you'll see the RPMs jump from 0 to maybe about 200. All of the fuses are intact , and my stepdad/free mechanic told me that the injectors were either running fully open or not open enough, which is an issue caused by the computer on the bike. He also told me that then again he could be wrong and that there could be hundreds of things wrong. Any thoughts? Thanks!

 

It could be that initially battery was weak and not generating enough current/voltage for the spark plugs. Although I am not too sure why it'd still be able to drive the fuel pump and not produce decent spark. But since then you say after charging bike cranks every time and occasionally comes to life, then it could be that you have a flooded engine from previous tries. Every time you try again, fuel is injected into the cylinder where there is some of it already which disturbs the mixture and the spark doesn't work. Do you smell petrol/gas ?Is the exhaust spitting out gas?Have you fiddled with the engine/throttle bodies in any way?
If yes then I'd suggest you try the WOT method to start a flooded engine.In case you don't know how to- Open the throttle wide open and push the starter button. Do not let go of teh throttle, keep it wide open and be persistent with the started button. Keep doing it for approx 10-15 seconds but if still doesn't start then I'd say give up and take the spark plugs out giving a chance for the gas to evaporate and then try again.

 

I pulled it out today to try to start it again, throttle fully opened and held the starter in for about 20 seconds before it caught. It was running for about 2 mins before I shut it off to get my riding gear, I went back out and started it up again, and it worked... but I shut it off again and now it's not starting again. It was idling around the standard 500 rpms the last two time I started it, but it whenever I would give it gas the engine seemed sluggish (for lack of better terms). Could i have just flooded it again or is there probably something else wrong?

 

Where are you from? Is it cold there now?
You should have let the engine run for at least 5-10 mins for the engine temp to creep up above 40-50C.
It could be that the engine is not breathing properly. An engine breathing problem, like clogged air filter or a leaking vaccum line, would affect the most at startup. The engine is stone cold so the ecu feeds the most fuel to the injectors at startup so the engine needs proportionately more air to burn the fuel and if it's not able to do that then it'll stall. Then when the engine temp builds up, the ecu feeds less and less fuel at idle eventually settling at the normal 1200-1400 rpm idle frequency. If the leak is not substantial(like a small tear on the vaccum line or not a fully clogged filter) then it should be able to sustain this idle rpm at 40-50 C and above.
You say standard 500rpm? That's way too low. You need to keep on giving it throttle after you start it up using the wot method till temp reaches 40-50C and the idle rpm reaches 1300 or thereabouts.
at startup, with your palm over the exhaust, do you see gas droplets?
Since you flooded the engine repeatedly, chances are your plugs are pretty foul by now, so I'd suggest use the WOT method, fire it up give it sustained throttle till temp reaches 40-50 C or so and then take it for a ride.That should dry your plugs and hopefully clear the soot and then you can investigate your vacuum lines.
There could be many things really, but checking your vaccum lines should be first. You can then inspect the fuel pressure regulator etc etc.

 

Sorry I couldn't reply recently as I've been busy with work and school, I can gave my stepdad my maintenance manual and he is sure that it's something with my ecu, he said that he can connect a wire somewhere and there'll be a series of lights which can tell him what's wrong with it which we're planning to do Sunday, if not the ecu we're going to take the air filter off so see if perhaps it is clogged (I put about 10k miles on it since I got it and it hasn't has the air filter changed since the last owner did it so it could definitely be that too). I'll post updates though! Thanks for the words!