With my A10-7700k, all I did was leave the bottom "half" (it wasn't exact) of the epoxy on the PCB. You know, the black crap. It gave me a guide for reinstalling the IHS, and when I torqued down the screws on my NH-D14, it resealed the IHS onto the PCB. Downside: I used CLU between the lapped copper IHS (yes, I lapped it after I popped it off, for good measure) and my lapped NH-D14. The copper <- CLU -> copper bond was so damn strong that when I removed the HSF later, it took the IHS with it. I had to twist it off the NH-D14 with some pliers. The epoxy reseal was strong enough to make it easy to seat the IHS, but it wasn't as strong enough to keep the IHS on the PCB. So that's a good thing if you really want to pop off the IHS again in the future. It's a bad thing if you use CLU on lapped copper surfaces like I did.
As far as protecting elements on the CPU PCB from conductive metal TIM, most of the people I've seen use clear nail polish over all the resistors and other crap sticking up above the PCB near the die. I didn't, and I had to use a ton of CLU to get good contact between the die and underside of the IHS, and I still "got away with it" somehow. Maybe I was just lucky, or really precise.
As to how much CLU to use, I tried using a tiny amount (as per my experiences when using it between the IHS and HSF) which did not work. The underside of the IHS was not exactly even. When I put in a ton of it (as per the technique I saw in . . . idontcare's old Ivy Bridge delid thread, or whatever that was; why didn't we sticky that?) it worked.