1) Document your old settings if you are pleased with them. But, you will have to set up your OC again. You have an advantage that you know what your chip will do, so apply that knowledge to your new motherboard.
2) Is there a reason why you are changing motherboards?\
3) Storing the old motherboard should be no problem. Even a paper bag would do, but since you have the wrapping for your new motherboard, that will do fine.
4) To make it easier to remove the cpu cooler, run your old cpu and motherboard so that it heats up and softens the thermal paste. That will make it easier to remove the cpu cooler without damage.
5) Protect what you must first, but I think windows 7 will start up properly on the new motherboard. Assuming it does, you will need to use the driver cd to update the chipset drivers.
6) Since there was a motherboard change, you will need to reactivate windows 7. No biggie if it was retail or upgrade. If the os was oem, be prepared to talk to MS and assure them that the os is being used on only one pc.