So I'm having issues with the bike starting I'll let you know what has happened over the past few days. I go out to start the bike it turns over a few times but doesn't start and then doesn't appear to have enough juice to keep turning over so I jump start the bike and then get to work fine. Same thing happens when I leave work. This also happens even if I put the battery on charge the night before, sometimes however it will start fine. Battery after charge is around 12.7V

Today had the same issue so jump started it at work and then got home, turned the bike off to drop off my bag and then got back onto the bike to get fuel. Started fine got a few mins down the road idling at the lights and the bike cuts out won't start again but the engine turns over several times. Then the battery acts likes it low as you would expect after turning the engine over several times.
I push the bike all the way home and then it starts fine even though the battery was down to 11.6v

I've had this issue before where it cut out twice when I was on a longer trip if I leave it for 20 mins or so it will then start again. I'm hoping these 2 issues are related.

Someone on here before said I should trace the pulse generator coil wiring and measure the resistance. Is this the right plug and is the multi meter set correct as I don't have ohms x 100 scale that he said to set it to

http://i1379.photobucket.com/albums/ah156/jimbob175/C8FB20EA-0E65-4743-8D8B-2582DB3CB9E4_zpsk9c6iak5.jpeg

http://i1379.photobucket.com/albums/ah156/jimbob175/086431F6-CE73-4E74-9BBC-C9006ADC6B45_zpswy6xlf0v.jpeg

http://www.bbburma.net/Documents/JohnBates_ChargingCircuitTests3.pdf

Is the battery new? It can be shot and still take a charge but it won't last.

Worth unplugging any of the wiring connectors and spraying with contact cleaner.

It's about 3 years old. The bike sometimes starts fine though and it did start when I got home, I had the battery tested 6 months ago because I had these problems and they said it was fine

It's most likely the following:

1. excess resistance in the alternator/regulator-rectifier/battery wiring due to melted or corroded connectors causing insufficient charge current
2. the battery is bad, even though you had it tested, they could be wrong or it could have gotten worse since the test
3. the starter is iffy due to corrosion on the commutator from excess heat trying to start it without enough current to turn it
4. (unlikely IMHO) the regulator/rectifier is "bad"

If you charge it overnight with a plug-in charger the battery should be >12.8V when fully charged and should be plenty to start the bike several times without needing a recharge. If it won't make a round trip (start-run-stop-start-run-stop) then the battery is bad. That doesn't mean it's the only thing that's bad. BTW my fresh AGM battery is 13.2V when fully charged.

If you don't have at least 14V during charging (2K rpm or so) at the battery terminals then the wiring from the reg/rect in both directions, towards the alternator and towards the battery, should be inspected to ensure the connectors are clean and not melted. They have a tendency to melt and corrode which causes the battery to not charge. Ideally this should be more like 14.4V FWIW. You will need a good voltmeter to test this, not just some parts store battery tester.

Frequent attempts to start the bike with insufficient current capacity will send the starter to an early death. This can look and feel very much like a bad battery.

Is it unlikely to be the battery considering it started fine after the long walk home?

At least I got a good workout, the gs is not that heavy but it does get heavy after a while

Just get a new battery. They can often 'appear' to take a charge and show good voltage, yet can't deliver the amps required to start up.
It's 3 years old. No use flogging a dead horse!

What does the voltage drop to as the bike starts, less than 11V and the warning bells should be ringing. less than 10 and the battery is borked even if it charges up.

If the battery is questionable, turning over the engine can take the lions share of resources, leaving little or nothing for the coils, leading to weak or intermittent spark.

So the bike started today and I was measuring the voltage on the battery when the bikes revs are at about 1.5k its generating 13.85volts when I take the bike up to 3k though its generating 12.97 volts, shouldn't the volts go up as its revs not down?

@Jimbob, I had exactly that problem, which turned out to be twofold. 1 I had a crap voltmeter, ended up getting a cheap Fluke 101, 2. I unplugged the wires from the stator and sprayed them with contact cleaner. Problem solved. The stator was supplying 60V AC on each of the three wires. So what does your V drop to at the moment the engine starts.

So I'm currently on the side of the road as the bike has stopped again. I took one of the spark plugs out and I can't see any spark but if I leave the bike for a while it should start up again

So the bike started again and doing 80km/h the engine stopped pulled in the clutch so I could coast somewhere and yep 0 RPM. Now waiting for it to cool down again

Definitely an electrical problem of some sort. When I had similar issues it turned out to be a bad signal generator pickup. The problem is when the bike is cool it will test fine. The only real way to diagnose the problem is to start replacing electrical items or run the multimeter tests after the bike has warmed up to the point that it doesn't work anymore. Everything will test ok when the bike is cold and that is not helpful. Hope that makes some sense.

I guess I can start by replacing that first, what other parts would I like at replacing?

Classic signal generator. The bike is 89-00 right ? then yes that will lose 1 cyl. The newer ones I believe have a single coil for both cyls.
Cool.
Buddha.

It's a 2004

Its got a single signal generator. You lose spark in 1 cyl or both ?
If its 1 cyl, its likely auxillary ground. Or other electrical connection problem.
Cool.
Buddha.

I think it's in both. The bike has 1 signal generator but 2 coils one for each cylinder

A mechanic said it could also be the CDI box, what does the CDI do?

Also I just replaced them signal generator so we will see how that goes