Ok, I've been reading this thread and it's just insane that it's not solved. You say the battery will only turn the motor over for 5 seconds. That is a bad battery, end of story.
You also write that if you manually run the points you get spark.. that's easy:
coils work like a battery that can charge up super fast, and then let it all out in one shot. If your battery is weak, it can charge the coils up slowly, and they still let it out all at once, but when you spin the engine, you need a robust battery for the coils to operate at the speed they're supposed to.
Are you hoping someone here can tell you how to make your bike run with bad parts on it? You'll be here a long time.