@thatmanfromspace the APU's have Worse Single threaded performance and overall lower IPC than the FX Line of CPUs if you Must have an AMD System i'd suggest migrating to an Ryzen build but thats the source of lag. yer PC is a potato in the eyes of Citra.
its like PCSX2, then Citra itself maybe running at the Desired Framerate but Not the internal GPU citra's emulating. (meaning your not really achieving 60FPS, i got a friend w/ an FX 9590 and they struggle like hell
if you want to build for emulation go for a higher end intel System it will Always smoke any AMD based system in performance its all a numbers game with Single threaded performance (amd lost this race many many years ago and they're kinda still like a few laps behind.) infact your going to have a hard time w/ that APU PS2 emulation w/ all the speed hacks on for alot of games (i can bet FFX would lag on you) let that be a sign that yes most AMD FX And APUs struggle w/ Emulation going that far back in console generations. (APU's have a better Multi-threaded performance over all but the 9XXX FX Series of CPUs and the FX's have better IPC/STP(SingleThreaded Performance) over the APU Line.
tl;dr, OP your PC is too potato and you need to upgrade to run citra, it's the simple blunt truth.