If you don't have the chain attached it will just idle in gear turning the front sprocket only. It would only stall if there was a good link between the sprocket and back wheel. If you are saying this is the case before you removed the chain it was either too loose to the point it had fallen off the front sprocket or snapped at that point. Are you 100% you have drive from the clutch? Can you post pics of the chain, pref in situ showing how tight/loose it is, and even better solution would be a video showing it all in place and you engaging first gear so we can see whats going on as its all getting a bit confusing as to whats happening.