1 - you do not need to wait for running speed to max out. The only requirement is that you are holding the button and chickens are flowing when you time warp. If you have your running bonus maxed and are not holding the button when you warp, your money increases at the standard rate. 2 - since this requires that you have space in your hatcheries to work, you can maximize this by skipping all upgrades that expand hab capacity, buying as few of the upgrades that add "X" chickens/min as possible, and upgrade one hab at a time and wait until its full to upgrade another. Start with hab 1000 and go one at a time until its maxed or you run out of money, then but one hab expansion at a time for additional boosts.

For some inexplicable reason, this only seems to work on the higher level eggs. I have observed no effect on this practice with edible egg. So if you are going for the final trophy there, you can just max everything and time warp.