ducati monster 900

I have a problem I would welcome some help with,
I have a 1995 monster 900, about 4 weeks ago I stripped the left case off to replace the gear selector spring (broken) while there I changed the other spring as well, I set up the adjustment what should have been good, rebuilt the left side case put oil back in, started the engine it ran as normal, but when I came to try the gears the up change was just not right.
I removed the case again to readjust the selector, did not have to remove flywheel, assembly can access the adjuster ok, came to start engine, would not run.
bearing in mind the engine had run normal first time rebuilt and I had no need to touch any ignition first & 2nd strip.
I have now checked every thing many times It will now only run on lower cylinder, have done carbs, checked belts, it sparks on both cylinders and will wet the upper cylinder spark plug.
I have bought a pair of ignition boxes and a different set of ignition pick-ups that came of a running tried the with no cure.
I am at a loss with what to try now, any advice?