Most pickups with factory-installed covers are wax potted to prevent microphonic feedback. Its possible to do this yourself, however it sounds like a lot of trouble and from what I hear, its easy to damage the pickup if not done properly. A bead of silicone chalk will prevent microphonic feedback just as effectively and is much easier to do. Here's the process.
To prevent the silicone from filling the holes and crevices, I place a piece of thin scotch tape over the bobbin. Use a bead of silicone about half the diameter of what I used in the photo below. If you use too much it can spread as far as the polepiece screws when the cover is clamped then you have a mess to clean up.
You can bend the sides of the cover in slightly with finger pressure to ensure that the cover contacts baseplate. It's also important to clamp the cover to the top of the bobbin as you solder. I have a couple of small hobby clamps that work well. The soldering iron should be about 25-40 watts. Be sure that the surfaces being soldered are clean or else the solder may not stick. A small glob of solder is all that's necessary to hold the cover in place. Don't build up a big glob as it becomes a heat sink and makes removal of the cover difficult.