Well today was rough, to say the least. I finally managed to get the killswitch under control.
Turns out, I used to wire it from the jack, hot to one side, ground to the other, and then through to the volume and ground.
But I went ahead and did what Andrew said, and it seems to work a bit better. Not as much popping, but there is still a very faint pop every once in a while.
My main concern was not being able to do it WITH the coil tap, but that wasn't even touched
The headstock got cleaned up as well, a few finish scratches, but nothing that noticeable.
(yes, I like to put the strings on backwards
I'd say it came out pretty darn good, especially for costing about $600