1. I am hitting the mun with about 1.8km/s less speed than launch DV so only losing about that, maybe only a tad more due to gravity drag. Also I don't think these rockets would handle a gravity turn very well.
2. Maybe, but that stage takes 5 minutes to burn, which probably nullifies the effect of the extra DV.. running a test now. The end result is 5 seconds worse than my sepratron final stage. I can't get it to fly perfectly straight with the ant and just parts attached on the axis of symmetry (how is that possible?), so it ends up flying a less efficient trajectory. Also you need a battery to allow you to disconnect the final stage for a burn that long, adding to the inefficiency.
3. I agree. my last rocket takes a long time to burn the first stage but speeds up significantly after.
the mass should be insignificant on the lower stages. On my upper stages the nose cone mass adds up to -20 DV (so I guess I'll remove them). It will be different for everyone obviously but I think the lower stages definitely need them. The part count isn't helping the real life launch time though.