All would appear to be correct at first sight . A closer inspection however revealed that the cog on the crank that runs the camshaft has moved . Weather this is pressed or pinned on I do not know. It means the timming marks on the cam shaft cogs are no good, and of course it could move again when the motor got hot , if I ever got it started. An other motor is the best option, but having difficuty finding one. Has anybody any experience of fitting a er5 motor in place of the kle? physically no problem I guess, but what do I need to change on the electrical side? I know I am a pain in the rear end but don't want to scrap the bike. All usful suggestions concidered.

well Chris I dont know if its pinned or what BUT, if its a pin that has sheared, its not too hard a fix. if its pressed and worked loose....its gonna play on your mind like a bad woman.
What would I do? I would get it all lined up perfect, then MIG weld the damn sprocket on! make sure it runs, then sell the bike to a non hubb member sharpish like and buy an XT......

Sounds like it could be that the cam chain timing is out, since you took replaced the camshaft and top sprocket. There's normally an inspection port down near the crankshaft to view the tick on the bottom sprocket (which should normally be at 12 o clock), and an inspection port (or possibly have to remove the valve cover on top) to view the tick at 12 on the top sprocket (RTM to be sure). Once both are at 12 o clock (ie Top Dead Centre - TDC) on the compression stroke (important!), you can re-check the valve clearance.

If the timing is wrong by 360 degrees (ie, you set it up at TDC, but not on the compression stroke), you'll get the valves coming down to meet the piston on it's way up.. not good! If it does actually manage to turn over without churning itself into a mass of tangled metal, it definitely won't fire up.

Incidentally, some systems have a "wasted spark" setup, where a spark is generated on both compression and exhaust (dependent on the ignition circuit setup).. so the important thing to check is the spark on the compression stroke (as per the excellent check in the previous post).

The CDI could have blown too.. if that went, you'd normally not get a spark at all (or if you did, it certainly wouldn't be advanced / retarded by the correct amount, for the load, engine speed, etc). The manual normally has CDI resistance tests in there that you can do, but the easiest way is definitely to switch in a known good unit. If you need to replace it, the Kawasaki OEM unit is expensive (I was quoted 290 GBP + VAT last week for one).. try this instead.. I've ordered one for my KLR.. IgniTech (130 EUR or so for a programmable CDI).

The sprocket is normally secured with 2 small bolts.. I'm not sure how it would move out of alignment when the motor got hot.

I agree with the last post; I can't see how that driving cog can be out of alignment because you have not changed it while doing your work (or have you?) - how are you so sure that is the case when you don't know how it is fixed in place?
Anyway, the important point is that the sets of timing marks are in alignment and the camshafts (plural - I guess you have two sets for a twin) are also aligned.

I did a similar job on a single cyl and the bike would not start when it was all back together - this turned out to be caused by me pulling the spark plug lead off so many times; even though there was a spark, it was not a strong one I guess (but it was visible in "shaded" light). Once I remade the connection of the lead to the spark plug cap and back to the coil it fired up.

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Dave

Perhaps the timing chain is off this bottom cog? This happened to me while reassembling the top of the engine - I removed the side cover, after draining the oil (some people say it can be done without draining by leaning the bike to the side) and managed to get the chain back on the cog by a stretch of the fingers, without taking off the flywheel/generator. Before that, I tried to get the chain back on the cog with a long screwdriver down the timing chain "tunnel" but it was jammed in and needed to be moved by hand.
Fortunately, I did not try to start the bike with the chain off it's cog - it was very stiff in turning over by hand with the kickstart, unsurprisingly! - that gave me the clue of what was wrong!

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Dave