The extra rice, koji, and water is not a problem. Just adjust/decrease your san dan shikomi additions to end up with 2 gal water, 10 lbs rice and 2.5lbs koji by the end.
Since you haven't added yeast yet, the moto shouldn't really be bubbling up. Most likely what you are seeing are the remnants of the rise and fall of the rice due to water absorption and then the subsequent decrease in volume due to liquefaction.
Vinegar is not a good smell in sake. Perhaps you could be mistaking lactic acid/koji aroma with acetic acid?
I think you should keep going with the ferment and taste along the way. Hopefully it will turn out great and not have any vinegar smell/taste by nakazoe and tomezoe.