It makes sense to waterproof first! Otherwise, you would have to remove the screws, waterproof, and re-screw.
Centering the Countersink: This is best explained by a machinist or engineer, but I will do my best.
On a countersink screw, the screw head has a convex conical bottom surface, not a flat surface. It fits into a hole in the mounting plates of the blade that has a concave conical top surface. Screwing the screw tight makes those two conical surfaces lock against each other, holding the mounting very firmly in place on the outsole of the boot. Both conical surfaces are called countersinks.
On a reasonably well machined screw, the entire screw and the countersink on it have the same vertical center, so you don't have to worry about them being different. On an optimally machined mounting plate, the mounting plate holes and the countersink on it would also be vertically aligned. But, a certain company that I will not name, which happens to make most of the world's figure skating blades, does not always machine things that carefully.
The rest of the hole in the mounting plate has no contact whatsoever with the screw when the screw is tight. Hence, if you center the screw on the hole - by, for example, pounding a punch into the leather in the center of the hole, then drilling the guide hole centered on the dimple you create that way - the pressure between the two countersink surfaces will push off-center, so plate will not be properly locked in place, and may shift around or come loose too easily.
What you must instead do, if it looks like the concave surface at the top of the hole is not centered on the hole (in which case, the top periphery of the hole is not a level circle, but is distorted in some way), is to guess where the center of that concave surface would be, and pound your punch into that spot. Just do the best you can.
I hope that was clear.
I didn't realize the problem existed until a pro showed me that typical mounting plate countersinks are not properly centered on the holes.
For a while, I thought of it as unbelievably shoddy workmanship, just as I considered the use of Phillip head screws, whose heads are so easily stripped, to be shoddy workmanship - before I realized how difficult it is to find #6 hex or square head screws.
It seemed poor workmanship to me because some of the people who mount blades at pro shops, have no more than a few minutes of training on mounting blades (much less than you have not spent trying to understand this), and can not be expected to figure all this out.
But now I recognize that such judgments by me are entirely unfair - after all, I'm not a machinist or engineer. Perhaps centering the countersink is a terribly complex operation.
If there are any machinists or engineers reading this, perhaps one can explain why it is so difficult.