What version of PCSX2 do you have? If it's a relatively recent one (and if it's not, then you should update), then you should be able to see if framelimiter is causing the problem by going to config -> emulation settings. Framelimiter stuff is on the GS tab. Also, remember that tab enables turbo mode (if framelimiter is enabled), which makes the game run (or try and run) at 200% speed.
With the speedhacks, there are a few you should probably have enabled, especially when you bear in mind that the CPU is the main bottleneck, not the graphics card. And even a GT440 can struggle at times.
The tooltips for the various settings give you a good idea of how safe they are, and how much benefit they give, so you can make your own judgements; I personally use all of them except Fast CDVD, EE cyclerate, and VU Cycle Stealing enabled, and I've never had any problems at all. A lot are game-specific, so they were sort-of removed from newer versions of PCSX2 - now it detects what game you're playing, and enables the game-specific ones as needed, so you don't need to worry about them.
