Please use nail polish remover to remove old loctite gel superglue!!! it comes RIGHT off! then clean off the residue left by the acetone/nail polish remover with isopropyl alcohol.
And yes, putting too much new silicon/rtv can possibly create a bigger gap between the die and IHS when doing a relid. This is why the 4 dot superglue method is recommended.
I personally like to sand down the part of the IHS that makes contact with the PCB to make absolutely sure the gap between the IHS and die is as thin as possible. Just make sure you don't sand it down too far where it becomes entirely flat.. although with a relid tool even then it shouldn't be that big of a deal. But the end goal is to make the gap between the IHS and die as small as possible while also keeping the mounting pressure even across the entire CPU PCB. I ran a naked ivy kit with my 4790k for a bit and ended up with a slightly warped pcb. Ended up just relidding it as the temps weren't even that great.
Edited by IMI4tth3w - 11/16/17 at 4:58pm