Yes, gaming motherboards will work. The only thing different on a gaming motherboard normally is beefier power hardware and some gaming/Overclocking features. In this case, I doubt there will be any overclocking done, but the beefier power hardware will come in handy keeping the pair for GTX 980Ti and the CPU happy. Paired with a high quality power supply, good memory, good storage devices, the system should be very stable for years.
You will have choices to make on the CPU. Do you want to go with X99 chipset on the 2011-v3 socket, using a I7-5930K or I7-5960X which are 6 core CPU's with 40 lanes of PCIe capacity, or even a 4 core I7-5820K with 24 lanes of PCIe capacity. These all use DDR4, which is a bit pricier than DDR3. And they all support 4 channel memory. Due to their 4 channel memory support, they also can have 64GB of RAM.
Short of that, there are the Z97 chipset with the 1150 socket CPU's, The I7-4790K would be the one choice for you here. 4 cores, 16 lanes of PCIe capacity, and still uses DDR3l. There is also a Broadwell chip... well, there is supposed to be... I just peeked at both Amazon and Newegg, and they do not exist there... So I guess the I7-4790K will have to stand alone here. With Dual Channel memory support, the limit here is 32GB of RAM.
There are also some Xeon CPU's that can work with both types of those motherboards. I would think that the two software packages you plan on running would support those as well.
If I were to do what you are planning on doing, I think I would stick with Asus on the motherboard. And maybe on the video cards as well. They do make some amazing hardware, and their reliability is second to none. They also cost a little more than some of the other brands. But in a business environment, uptime matters. I would probably go with an X99 system. Not only are the CPU's stronger, but they offer more PCIe lanes, which will allow each of the video cards to have a full compliment of 16x PCIe lanes. On the 1150 boards, they would only get 8x PCie lanes each. That may not be a big deal for gaming, but it could be with AutoCAD. And as far as the CPU goes, I think having 2 additional cores, so 12 threads maximum should help with the workload. So I would pick the I7-5930K CPU. It is a slower version of the I7-5960X, but also about 50% of the price.
In looking close at the motherboards, trying to pick something that should work well for you for a number of years, I have focused in on the Asus Sabertooth X99 motherboard.
I will let you look it up, and see what you think about it.
This should give you a bit to consider. Let me know what you think so far...