Dude, I just can't figure out what exactly you're saying. Could you please just try out Ishiiruka once (you don't have to overwrite Dolphin proper, just make a new folder) and see if the issue is still there? If it's gone, then shader cache stuttering was your problem and it can not be fixed in Dolphin proper at this point (just keep in mind that Ishiiruka is an unofficial build and you will only get support for it in the Ishiiruka-thread).
Intel i5-4690k (Devil's Canyon) @ 3.5 GHz (+Scythe Mugen) / Gainward GTX 1070 Phoenix (OC'd) / ASUS Z97 PRO GAMER / 16GB G.Skill DDR3-2400 CL10 TridentX / X-Fi XtremeMusic / Win10 Pro 64bit / Dell S2716DG Monitor / 3x original WiiMote+MotionPlus+Nunchuk