So, a little update!
Swapped out the HDD to a bigger 750GB HDD and installed Win 7 on it, along with super resolutions. Switching from different resolutions is much smoother now and games displays perfect.
I also recalibrated the monitor and found out that it was too dark. I adjusted the brightness, contrast and was able to see more details in dark areas. Now the snapshots in Mala looks even better! So I did some F12'in and grabbed some snapshots from the games in my list, added a black layer with 50% opacity on all the snaps and now Mala starting to look pretty good. I skipped videos, it's just too much work.
I'm pretty happy with the layout in Mala and it works great
BUT now I have some kind of slowmotion/audio stutter problem? I think this is because of the super resolutions and I didn't experience this before. For example, DoDonPachi says: "Countdown begins, three, TWO, one, GO!". The words in CAPS are in slowmo so it's not constant slowmotion, it's like a wave, slowmotion comes and goes. I haven't checked if my CPU is maxed out yet and I read about using frame_delay (I have it disabled) can cause audio stuttering if you don't have a good enough graphics card. So I'm starting to think it the graphics card after all. I need to do some more troubleshooting.
If you guys have any ideas, please let me know!EDIT: Added a link to my gamelist in the main post. Feel free to recommend some games I've missed.