No.1 no as they should be on the memory cards, and afaik installing the latest version doesn't overwrite them, i would advise making copies of your saves and putting them in a different location
the memory cards are usually in C:\Users\
whatever you call your pc\Documents\PCSX2\memcards\Mcd001.ps2 Mcd002.ps2
although if by saves you mean savestates they won't work on the latest 1.2.1 as they aren't really interchangeable
No.2 yes of-cause you can back them up

, i often back both savestates and memory cards up, but as stated above savestates aren't really interchangeable
to see what's on them go to CDVD and then where it says No disc click their and then go back to System and do a full boot and voila
when your done just go back to CDVD and put the dot back where it was
No.3 hm it all depends on what pc you have, but generally i'd say yes it's a lot better
hm Grove4L kinda beat me to it
Not sure what graphics card you have, it's memory bandwidth,
it's temperature, fan speed, what pixel shader it has
try TechPowerUp's
gpu-z
Not sure what your cpu is try
cpu-z
(hint click on the highlighted links

)