If nothing else seems off...
Could be a defective new EOS switch, I've had new switches that were shorted internally.
Maybe try the old one and see if it's better and then order another new one?

I think with these two wires it really doesn't matter if you switch the wires on the lugs on the switch.
It's a normally closed switch with two wires that should open when the flipper is in the up position.
So either way it opens the switch so really shouldn't matter.
Unless those wires are going to the wrong place on the coils but I think that has been verified.
All I can think of is that coil somehow got shorted or there is a cold solder joint on the thin wires coming from the coil itself.
Maybe a new coil or taking a closer look at those connections.

That is odd but perhaps those parts just wore to perfection! LOL Only thing else I could think of is there was some slop in the coil bracket or coil stop causing the buzz with the new parts. Coils get kinda warm when holding the flipper, a lot so unless it was getting really hot it might not have been an issue, but that buzz is annoying. Wonder if you put in the new parts made sure all was snug, and the coil could not move at all in the bracket it might stop buzzing after you play it for a while. Like when the new parts get broke in a bit. Anyway, sounds like you at least eliminated any miswiring or short issue or anything.