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Hi friends of the internet!

I had some issues concerning my build (specifically the graphics) that I could not get answered based on basic searches.
I was hoping some of you could clarify or even fix some of the issues I am having.

First my build is:
CPU: AMD FX-6100 (OC-ed @ 4000GHz)
CPU Cooler: Corsair H70
RAM: G.Skill Ripjaw X Series 4x4 (16 Total)
Mobo: MSI 990FXA-GD80
GPU: ASUS GTX 660TI (OC-ed @ +100W, 120%PL, +125Clock, +500 Mem using Afterburner)
GPU: ASUS GTX 660TI (OC-ed @ +100W, 120%PL, +125Clock, +500 Mem using Afterburner)
GPU: Gigabyte GTX 460 (Stock @ 715Clock, 1800 Mem)
Case: NZXT Switch 810
HDD: WD Blue 500GB
HDD: WD Blue 500GB
SSD: OCZ Agility 2 120GB
Monitor: ASUS 24 Inch (VIA HDMI to GTX 660TI)
Monitor: ASUS 24 Inch (VIA HDMI to GTX 460)

So the issues I have are follows (and what I have been able to gather about them)

1: Lock Clock. The default seems to not be at the clock that is printed. Right now, with MS Word and 2 Chromes open, it sits at 967 MHz and goes up to 1267MHz during stress testing (Furmark)
However, during games, it stays at 967 while giving less than 60 FPS. I don't understand why this happens. I did gather that the GTX 660TI stays at low clocks but increases as load increases. However, why is the load not increasing when playing games where I am getting less than optimal FPS? (I test this in FFXIV where I am getting ~30 FPS in crowded areas)
I would also like to tag onto this that during stress test, the Clock fluctuates in the ~1250MHz area, going up and down constantly. (I also gathered this was normal?)

2: Multiple Programs cause FPS loss. I understand if I was running Something like... Starcraft 2 and FFXIV at the same time that I may see less than optimal FPS, but I am talking about things like... Having a game on one screen (FFXIV, SC2, or LoL) and a stream or a youtube video on the other screen. It causes the game to suffer immensely in performance. For example, FFXIV seems to drop under 30FPS even in uncrowded areas and LoL seems to drop to sub 20 FPS. When I close the other program completely (Chrome) the game performs perfectly, reaching a stable 60 FPS (VSync Enabled). I assume that the of a stream ( or Youtube) should not be causing so much load on a SLI GTX 660TI Build that it makes my games on my other screen suffer.

3: Multi-Card. I had a build of two GTX 460s in SLI, but upgraded to the 660TIs. Seeing as how I had the room, I decided to throw one of the old 460s in the build as well. Is this a good idea? I did this because I cannot connect 2 monitors VIA HDMI because I cannot connect two HDMI to 1 card and for SLI I cannot connect monitors to different cards. Is this configuration of 2 GTX 660TIs and 1 GTX 460 a problem? This also leads into the next question.

4: Physx Dedicated. Since the 460 is added, I had it selected as Physx dedicated. I read that it does not increase performance by that much, since the 2 GTX 660TIs would be able to handle such load of Physx, but since I had it doing nothing but possibly collecting dust, I threw it in for any thread of performance increase. Is this a mistake?

5: I am running the GTX 460 under default, but I had noticed that sometimes the card is being overclocked. (I am using rainmeter to pull the information from Afterburner.) Setting the 460 as the default card and changing it back to default sometimes fixes it, sometimes does not. Anyone know why this happens and how to prevent it?

Thank you all for reading and helping if you did. I will supply any additional information requested.
Please ask, I do not know what else to supply.