The difference between 8x & 16x PCI-e slots is negligible. What is more of a limiting factor is what processor you are running & at what speeds. Pretty much any AMD CPU will bottleneck 2x 760's to an extent on CPU bound games. Being someone who owns both a system with an i5 3570k and a system with an FX-8350, I'll tell you first hand, the Intel will destroy my AMD system in an SLI setup, at least in CPU bound games that aren't very multi-threaded. However in games like Crysis 3, Battlefield 4, and other games alike, you probably will hardly see much difference unless you plan on playing at 1024x768.

at 4.1Ghz you should see a nice difference when SLi is enabled with the FX-6300. I'd personally grab a benchmark program like Unigine Valley benchmark, and run it, without SLI enabled, then run it WITH SLi enabled. See if you see much difference.
https://unigine.com/products/valley/download/
 Download and run that, and report back with results. I'd say you should be seeing roughly 35-40FPS increase at 1080p with dual 760's on that particular benchmark with a FX-6300. If you run it and see no gains, you have an issue :) at least then you can rule out an SLi issue. BF4 doesn't have the best SLi scaling, but it's not terrible either. I run 2x 670's which is essentially the same performance and chip as a 760, and do see a very noticeable difference in BF4.

Wow man, that really doesn't seem right!
On my other rig, running an FX-6100 @ 3.8Ghz and 760 at stock clocks my results were
36.7 Average
MIN 16.6
MAX 71.6
 
My primary with 2x 670's(basically a 760) on the extremeHD setting scores
82.1 Average
34 Minimum
150 Max
 
Stupid question, but are you running an SLI bridge?

those scores are why I was wondering if the fact that both my pcie lanes are at 8x when running sli could be a factor.

I will have to do some testing when I get home to try and see if my cpu is holding me up

I suggest giving 3Dmark 13 a go, you should see much more of a difference as valley doesn't have the best multicore support and 3dmark will use all of the cores.

tufgriz
power supply wise I am running antec 750.    Correct me if I am wrong, but if it was low on power,  wouldn't it crash?

Yeah, that psu is fine. And yes, if it were low on power it would crash.

 
Hmm, that's a really low score. It should be in the 9-10K range. 
From that I can see the cpu is really limiting the overall score. What cooler are you using? The only thing I can think of is that it's throttling from heat and/or it's not reaching it's max clock speed.

Now, the physics & graphics scores are what I would expected them to be for your system. 
Try it with 2 cards again, the first run might have been a fluke.
 

Okay, that's definitely a cpu bottleneck. Overclocking it to 4.3-4.5GHz should help quite a bit.
Try it and report back.
 

well its looking better, this one the cpu is clocked at 4.3

I briefly saw it up around 92%
 

well, this pretty much solves the issue's now lol  Did a little bit of an upgrade
http://www.3dmark.com/3dm/4964649?