The 0.1Ghz won't make any difference, but the extra 2MB could. Of course, it depends on how you use the machine. If you are routinely doing demanding CPU processing/number crunching, it could shave off some seconds from you workflows here and there. If the price difference is negligible and you do intense work on your machine, I'd take the one with larger cache. If you use it for more casual stuff, don't bother.
I saw some refurbished Mac Pros from Apple some of which had this
Dual AMD FirePro D700 graphics processors with 6GB of GDDR5 VRAM each
Based on the excerpt above it appears that both graphics cards have 6GB of GDDR5 VRAM making a grand total of 12GB of GDDR5 VRAM between both cards. The cheapest version with the dual 6GB graphics cards is $3,339.00 with 256GB SSD and 16GB memory. The next Cheapest is $4,249.00 for one with 32GB ram and 1TB SSD. Both of which has the 3.0GHz 8-Core Intel Xeon E5.
.1 gHz isn't going to be noticable at all imo. I think we're well beyond measuring the speed of a computer by it clock rate. For simplicty sake, I'd probably opt for the stock model that has the configration that you mentioned.