Well the quality of the bark determines the maximum yield you can achieve. You can only extract what the bark contains, some bark is probably of a lower quality than others and will contain lower alkaloid content. Using a larger bottle on its own is not a problem, but adding the extra water will lower the pH, but I doubt it will have affected the yield too much. Buy a pH meter so you can always assure yourself you are at the correct pH, that way, if you end up with a poor yield, you can concentrate on what other variables may have caused the low yield.