I increase from room temp to incubation temp over time by using a "slow" incubator...one with low enough wattage so that it doesn't work like a convection oven to heat the eggs too quickly. In my cabinet, I am using 11 watts/cubic foot with forced air, my old Farm Master incubator was 13 watts/cubic foot forced air, and my Leahy is 41 watts/cubic foot with still air (fully radiant top panel design).
pH reference: a more alkaline environment for development will help fight bacteria. Two references on this topic:
http://www.thepoultrysite.com/publi...handbook/5/internal-and-external-egg-quality/
http://www.biolbull.org/content/57/5/300.full.pdf
Air cell growth is certainly not "complete" by the 2/3 or 3/4 stage of incubation, however the chick's size to shell volume should be managed to this point so that the air cell can finish developing in the last stages.
I agree that weighing is key. But from a practical point of view, as in any production analysis, a few samples will suit as long as they are chosen without bias to the preferred result. So marking a few on day 0, then tracking the weight throughout incubation, will serve the end result. A notation of air cell development while charting weight will show that the charts are quite reasonable. Drawdown of the air cell down the side of the egg between day 14 and day 18 (or 24-28 for turkey) is dramatic and essential to a reliable pip, and can only be accomplished if the chick does not occupy too much shell volume and has sufficient moisture in-shell to prevent shrink wrapping.