You do realize that you can see your temps VIA MSI After burner or ASUS's GPU drivers for the GPU..Right? Or ASUS's GPU Tweak tool as well I believe (Haven't used it, but Zotac's GPU tool list the temps and such)
If your temps aren't that high at all (below 80'C usually) you shouldn't be experiencing any issues in performance at all. Unless it could be either a driver issue (Make sure your Nvidia drivers are up to date, Don't install the ones off of ASUS's website, if you did, Uninstall them pronto, and install the updated version off of Nvidia's website)
To much thermal paste on the CPU won't cause any damage, as for the GPU, to much thermal paste STILL won't cause any damage really. JayTwoCents made a video about this particular problem to, as to much thermal paste usually only applies to CPU's, not GPU's. Just to clarify.
https://www.youtube.com/watch?v=rAid5G30-WM
(He used a GTX 660 for this video, and the temps even went down by 3'C because he used way better thermal paste VS the manufacturers thermal paste which is usually cheap stuff)
To much on the CPU tho could increase temperatures depending on the type of thermal paste you use. As for the GPU, it usually doesn't matter (your manufacturer spreads so much thermal paste on those cores that it touches all the major pins and so on, but nothing shorts out. Just make sure you use non-conductive thermal paste, not conductive)
Also, depending on what the on-board graphics where, if you did a fresh install of Windows they shouldn't be appearing at all anymore. Meaning they'll never install again, so what? You'll have to re-install Nvidia's drivers though. Afterwords, you should be fine.