I am not a Hardware expert, I am just a freelance animator - so please advice that my opinion reflects only my own opinion.
The board doesn't matter - as long as it's not sub-par and AS LONG AS IT'S WORKING...
I chose my board to what had at the time the best reviews / price, and I have been using Gigabyte forever and they were good. Asus has a great reputation - however - whichever board you DO decide on - make sure to check reviews both on NewEgg & Amazon - some X99 boards have been very buggy to many people.
Make sure to choose your memory especially from the main board's QVL & that it will support 128Gigs RAM.
128Gigs sound like an overkill just for Houdini - but I might be wrong about that. 128Gigs I would think only heavy editors working on RED and 4K footage might need...
In any case - I would go for a 64GIG kit, setup your build and see if in your workflow you use the entire 64GIGS, if so then for sure upgrade to 128 - upgrading RAM is VERY simple, just a simple plug&play so I can't think of any reason not to try 64 first.
As for Houdini simulations - check the balance of your CPU, RAM and GPU - find the bottleneck and upgrade THAT component, I doubt it's the RAM....
Quadro vs GTX is an endless debate.
I am not a hardware expert, so feel free to look at posts at hardware forums such as tomshardware, anadtech, etc.
From my 6 years of experience: NO, GTX cards are always going to be faster, and they cost about a third to a quarter of their equivalent Quadro counterparts.
Quadro's selling point are optimized drivers - this will result (supposedly) in more accurate viewport display (the window used when actually working in a 3D suite).
If money is not an issue - go for it! but as far as speed & rendering - you won't get any value added.
Also - note that most rendering is done on the CPU, and even current GPU rendering sends calculations to the GPU - so the results should still be good.
If your are using 'Maya Hardware / Maya Hardware 2.0' for final frame rendering and accuracy is extremely important you might want to consider a Quadro as well.
Again, I myself am an animator, not a hardware expert so all this is said with my own experience, since I am on a budget, and I purchase a new build every 5+ years I try to both get the best Hi-End system I can without completely breaking the bank, so I use the GTX cards, always had. Both Autodesk and Adobe would still recommend Quadros but testing is still done on GTX cards and some are still certified.
Autodesk MAYA 2016 - 2017 Certified Hardware
Autodesk Certified Hardware website
They are (as mentioned, already using this for 2.5 months)
As for after effects - the CPU and GPU (unless using specific plugins such as Element) make little difference, a much cheaper option of both would probably made very little difference).
After Effects is very RAM hungry, and disk hungry.
When After Effects is required to read in realtime Gigabytes-over-gigabytes of footage, and/or image sequences comming from 3D renders the read speed of the SSD makes all the difference.
The truth is that the 960Pro wasn't available anywhere at the time I bought this, so I "settled" for the SM961, but turns out that in some cases it even beats the 960Pro.
The one downside of it is the lack of support: Firmware update and Samsung Magician are off limits, unfortunately.
Performance-wise it's incredible.
On a side note, I got 50% on it...
Besides, AMD Ryzen is completely new, and not tested enough in the community of CG.
Being an independent freelancer, I frequently use forums for tech support since I need to quickly be able to fix issues I have, all this community is on intel so support is easy to come by.
I am using this system for work and the software I use (tested at studios I go every once in a while) AMD workstations can't match intel's performance.
Seems though that they are finally getting there.