If you are having microphonic problems without the cover, I would first try to solve the microphonic problem by checking a few things.

Make sure both bobbins are firmly secured to the bottom plate.
Carefully tighten the 4 bobbin mounting screws. Do not over tighten or strip the mounting holes in the bobbins.
Make sure the magnet is firmly secured and does not slide back and forth.
Make sure the pole pieces are not loose in the bobbins. They can vibrate and cause feedback. Especially in bobbins where the neck of the screw isn’t secured.
Make sure the stud pole pieces are not loose.
Check to see that the metal spacer is firmly secured between the bobbin and bottom plate.
The height adjust springs can vibrate and cause noise or interference with the pickup.
Make sure the pickup is firmly attached to the mounting ring. Pickups that are loose in the mounting rings can flop around and also make unwanted noise in the instrument.
I don’t like to wax pot various models of pickups because it can change the appearance or decrease the value of the pickup. If the parts are loose try using a small amount Vaseline to lubricate the metal parts to cushion the vibration that can cause feedback. It is easy to remove and will not damage the parts.
Wax potting should only be done by an experienced repairman under controlled conditions because of the safety factor and damage that could occur with the plastic bobbins.
Installing a metal cover should be done with proper clamping to firmly hold the cover while being soldered to the bottom plate. Having a cover that is loose on a pickup will only increase microphonic feedback and should be carefully wax potted, quickly and preferably in a vacuum system using specified temperatures.