I've got a 1995 Kawasaki KLR250 D12.  I've recently had the frame powder coated and fitted some new parts to it and also put parts of a new wirirng loom on. Now I have the problem of the bike runing but cutting out when it goes in to gear, I've by passed the side stand switch and it still cuts out when going in to gear. I've also noticed that the headlight flashes ahen the indicators go on but I have made sure there is a good earth on the frame. The cooling fan also seems not to be working. could this be part of the same problem? If any one has any ideas I would be greatfull.                                                                                                                                                                                 

Cutting out when going into gear nutrel light switch ? The lighting could be bad earth so try running earth leads to all lights from a common earth plate fed by the battery                                                                                                                                                                             

Sidestand switch and clutch lock out switch are usually interconnected so you may have bridged the wrong wire on the sidestand.
If you've been powdercoated check and clean all earth points on the frame!
Does the fan work if the thermostat is by-passed?

I've fitted a new neutral light switch and thats working and the earth is good as I have removed the powder coat from the earthing point.                                                                                                                                                                              

This may seem daft but check the bulbs are correct if you have the wrong type fitted it will cause all sorts of strange things to happen. not talking about wattage more the single/double fillament                                                                                                                                                                             

All the bulbs are correct wattage, now, the Fan switch is knackered so I'll need to change that and the Battery is shot too.                                                                                                                                                                              

Make sure there is a good earth connection between the back and front of the bike. i.e. run an earth wire between them if there isn't one there already. 
What JP said would do that though.                                                                                                                                                                             

priced up a Rad fan switch today, £70 I had to pick myself up off the floor! lol                                                                                                                                                                             

(I'm no meshnik) but from what you're saying I would trace some of the wires from start to finish.. could be caused by a wrong connection(?)                                                                                                                                                                              

I think there an incorrect connection somewhere if u sorted the earths an checked the bulbs are the right type (not wattage.type). You say u replaced some wiring......hmmmm could this be the issue? double check it. Have u a wiring diagram for the bike?                                                                                                                                                                              

I by-passed the clutch switch and it ran perfectly, all I have to do now is see if it will run with the wires switched round.                                                                                                                                                                              

I've sorted the problem out now, looks like the clutch swith wasn't working, so I've soldered  the two connection together and it's working fine now. Thanks for your help.                                                                                                                                                                             

so you have bi-passed the clutch switch?? That might be an MOT fail as it is generally considered a safety feature. Personally i would replace the clutch switch.  Have you still disabled the side stand switch??
example 1 - you cannot see the neutral light or are not looking when you start the bike. Bike is in gear and you don't pull the clutch in. Discuss                                                                                                                                                                             

I can see what your saying Pagan but Im sure that at the minate there is no check on these devices but there are changes coming to electical systems and repairs that may affect it. I along with alot of members remember saying WOW its got a nutral light I always pull in the clutch before starting most bikes                                                                                                                                                                              

So do I and the same on the car. you never know if it is in gear  and it puts less stress on the starter and battery not having to drive the gearbox too                                                                                                                                                                             

Not an mot fail as the bike doesn't need to be started for an mot, in fact if the exhaust is standard it doesn't even need the engine to be in the bike, just present so the numbers can be checked!

                                                                                                                                                                             

Thats good to know as i think my exhaust gasket is on the way out. so take the engine out and i am sorted.                                                                                                                                                                             

Blowing exhaust gasket may burn out your valves but won't fail an mot, instead of wasting time trying to get the engine out with the exhaust on, its probably easier to fit a new gasket!