Bike running badly

I have a 2006 St1300 which has only covered 10,000 kms, has been laid up for a couple of years.
Unfortunately the petrol went rotten which had clogged up the fuel pump and turning the lower fuel tank to varnish.
After cleaning out the tanks and replacing the pump and spark plugs.
The motor starts with difficulty but runs with a miss.
No error codes appear as described in the workshop manual through MIL.
One would think if it was an injector it would show as a error code ?
The been has always been sheded and was running well when laid up.
Any clues?
Cheers
Aussie

Is she firing on all 4 cylinders? see if all four headers are getting hot,could just be a bad plug/plug lead or coil problem,
some fuel additive like seafoam might help clean up the internals.

Run some fuel injector cleaner though it a few times.
If the tank is rusted, there is a solution you can mix up to raise the PH level, hook up a battery charger to the mixture and remove the rust down to the bare metal.

You tube:
how to clean your fuel injectors

And

https://m.youtube.com/watch?v=-WuU1F2VLoI

Or by electrolysis, this is the way I cleaned a few tanks.

https://m.youtube.com/watch?v=SyG0mu2T4u0

You may want to put some SeaFoam in the tank as you may have an injector that is partly plugged up with gunk from the old fuel. I hope you did not have the mice in the "V" area chewing any injector wires. You may need to check your spark plugs also. Good luck.

Always good to check al the basics first: Compression, Spark, Fuel.

Use a crayon or other wax on the exhaust header, if it melts your firing. If it has no MIL it is possible you have no fuel going into one of the cylinders. If it were spraying fuel in into the "bad" cylinder but not igniting it, it is likely the O2 sensor would pick a rich signal and set the MIL on.

Check for good connection to the injectors and check all the ground wires. You can use a Noid light (Example: http://www.amazon.com/Lisle-27800-Universal-Noid-Light/dp/B0002SR57Q) to check pulses to the injector. If the pulses are good, you have spark and compression, you may have an injector problem.

Best of luck,

Keith

Thanks fellows for all your input I went down Keith's note on exhaust temp using a Themo gun which came up with 1 & 4 cylinders not heating.
I feel reasonably confident that the problem lies in the injectors. Not sure why there is no error number?
There is no sign of moisture or rust in the tanks only the smell of foul petrol.
No rats or mice have been in the shed.The bike was ridden into the shed and just left with a trickle charger on the battery.
Aussie

The injectors will only set a code if there is an electrical problem, open, short, high resistance etc. If they are simply clogged the computer cannot tell. The computer could set a rich code but it would have to run long enough to heat up the O2 sensor and that is not going to happen if there is no fuel to ignite. It does sound like plugged injectors.

All's good have the ST singing on all 4 again.
Removed all injectors from the bike then after removing the o-ring on the input end a foot of 3/8" tube is fitted over the neck.Held vertical it was half filled with carb cleaner.
Then my assistant pulsed power into the electrical posts via a battery whilst I blew into the plastic tube. The two plugged up injectors took a bit but eventually cleared.
Cheers Aussie

Great News!

Good to hear that you found the problem and got it taken care of.

Very ingenious, I like your method!