Re: make single conductor 4 conductor
The cover isn't that much of a problem. Ideally use some desoldering braid to suck up the solder beads and just lift the cover off. If the wax is heavy, it can stick a little bit but it will come off.
But proper desoldering requires a pretty hot iron and most folks in here are using just a 25-watter so you're likely stuck with one of the other methods that require some force to break the solder joint -- and will likely bend the cover a little at the bottom as uopt says. But that doesn't show when the pu is installed in the guitar. Only issue maybe for re-sale.
If the pickup is potted post-cover, there should be enough wax on top of the coils or stuck to the inside of the cover that there's no need to re-pot. If not, you can always add a little wax, no big deal. You're just trying to keep the top from vibrating and a bit of wax, silicone, or thin foam or who knows what will do the job. Re-dunking is just not necessary.
You do NOT have to directly deal with the coil wire -- if you do, if you even SEE any coil wire (other than maybe some peaking out slightly at the edge of the coil tape), something has gone horribly wrong.
THE NITTY GRITTY
Each coil has a start lead and a finish lead. With most manufacturers (myself included), the start lead comes out of the bottom of the coil and the finish lead comes off the side. 2 coils with 2 leads means 4 total leads -- those are your 4 conductors and the conversion is just a matter of soldering these 4 leads to the 4 conductors in the 4-con wire. (The 5th bare wire is soldered to the baseplate of course.)
There are two tricky parts, one mental, and one physical:
1) Physical: Separating the coil junction leads. Many winders solder the two finish leads together. Some of us, like me, solder the two start leads together. Either way you need to desolder them very carefully, don't put any significant stress on the two leads. If you yank out a finish lead, it's a pain but fixable. If you yank out a start lead, the coil is DEAD and only a complete rewind will resurrect it. NOTE: The start lead does not have to come all the way out of the coil for you to have killed it!
The other two leads are pretty easy, one is soldered to the baseplate and the other is soldered to the center (hot) lead of the braid. You can just heat the baseplate lead solder joint and remove it easily. The other one can be just clipped off so you don't have to worry about yanking it loose from the coil.
2) Mental: You can solder each lead to whatever color of the 4 cons you want, as long as you know that you know that you know which coil lead each color represents. If you want to duplicate the Duncan code, it is:
Green = Screw coil start
Red = Screw coil finish
Black = Slug coil start
White = Slug coil finish
The final issue is keeping the whole wire nest neat. It's tricky to explain that part, you just have to have to get some experience with it, and besides there are other winders who are better at it than me.
On the whole, it requires some patience and some fine motor control. It's not for everyone to try, but if you're aware of the pitfalls, have steady hands, and get the concept of start vs. finish leads and have some solid basic knowledge of how a humbucker works and is constructed, it's very doable.