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Hot wires and possibly a duff battery?

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I have just put my 2A Commando back together having replaced front and rear Isolastics amongst other things. On Friday I got it back together and it started first kick - but the AO red light didn't go out. This is supposed to go out at 12.4V  so a quick check with the multimeter and sure enough, battery sits at 12.24. (It's been on an Optimate charger throughout the rebuild of the bike) I put a bulb across the two alternator wires and the bulb glowed bright in response to an increase in engine speed - so the alternator is charging. Reconnected everything and got the bike going again. Checked battery volts and discovered 11.94V on the multimeter despite engine revs. Worryingly through - the alternator wires are now quite warm to the touch! Switched everything off again and rechecked the battery which appeared to have recovered to 12.2 V. Stumped as to what to do next I put the multimeter between battery positive (earth) and a good earth on the frame, set to 10A DC and on the 20ma scale, ignition off, and discovered a reading of 4ma. I may be wrong but I thought that this was indicative of a drain on the battery, that is to say something is taking current when it shouldn't be?  Having now reached the limit of my electrical know how, such that it is, I would really appreciate some words of wisdom as to what the cause of this problem might be. Given the recent reassembly I suspect that it will be something I have done (or not) in the rebuild? Thankyou for your attention.  Dave
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Please ignore the comment about 4ma - I blame operator error!
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I suspected as much. The bike has been laid up longer than intended and hence battery on the Optimate longer than planned. It would not be the first time that I have had to replace a battery after extended Optimate support - never again! Thank you for your response.
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Yes the Optimate type of battery charger cannot be trusted, They say the voltage is HIGH and therefore fully charged when the voltage is high, but there is NO POWER in the battery. The first action when you are in this situation is to put the battery on a REAL charger where you can SEE 2A going in for 1/2 a day. Attempting to measure current in these situations if you are NOT sure of how such current checking works it is best NOT TO. Alternator hot wires? You do not say what your charge system is original rectifier/Zener or replacement reg/rect. The former should NOT have hot alternator wires unless the rectifier has part failed. The reg/rect system can have warm alternator wires BUT you haven't done the full alternator test as per A O Services.co.uk    
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I bought a new battery and the bike fired up first kick - and then cut out after a couple of seconds and has not started since. I have been over pretty much everything I can think of in both electrics and fuel and remain baffled. All I get is an occasional popping back when I kick it. Incidentally I also get the (AO) warning light on immediately after an attempted kick start, and then it goes off again.  I suspected the Boyer ignition unit but it appears to pass the test of creating a spark at the plugs when making and breaking a connection between the two stator leads with ignition on? Only other relevant point I can think of is that my multimeter displays 0.3 - 0.4 ohms between battery (+ve) and every earth on the bike. It's not a lot but I would have expected this to be zero?  I would appreciate any suggestions toward solving this mystery.  
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... rarely zero properly. It's best to see what it reads when you connect the probes directly together. Apart from that, I would jury-rig a system bypassing the main loom to feed the Boyer direct from the (fully charged) battery protected by a simple fuse. That would then tell you whether the Boyer was working. If so, start a process of elimination. I would also consider whether your warning light is correctly wired.
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Today I ran a fused live direct from battery to the Boyer ignition box as suggested and the bike still refuses to start, although did produce quite a pop back at the end of one kick. Other than that the only sign of life was when making and breaking the contact with the battery which must have caused a spark which produced a small backfire through the carb. So at this point I am inclined to blame the Boyer box - which was on the bike when I bought it 30 years ago so has not done too badly.
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It is of ltd usage trying to start the bike if you haven't got a spark just when you want it ie correctly timed. You do not need to keep kicking to find the spark, pass a magnet across the back of the two silver coils on the pickup plate. (This is the same function as the two magnets wizzing around inside) It must spark.

 


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