What year and model BMW motorcycle do you have?
You have an Enduralast Ignition? Have you checked the timing with a timing light?
Did you do ANYTHING to the carbs?
You have to start at the beginning. It may not seem that this is necessary to you but it is. Adjusting the valves is first. Since you have electronic ignition (?) I think, check the timing at idle and at full advance, 3000 rpm is number two.Since you haven't done anything to the carbs (probably don't know a thing about carbs, or do you?) Check the operation of the floats and see that the float needles seem to be sealing, number three.
This may get you started. You are going to need a manual. The Clymers or the Haynes manual will do but you do need a manual.
You had the carbs off is very likely they are not installed completely or otherwise are leaking vacuum. Leaks in the tubes between the carbs and the engine will cause the symptoms you have.