Here's something you can consider, with focus on small size and silent operation:
PCPartPicker part list /
Price breakdown by merchant
CPU: Intel - Core i5-8600K 3.6GHz 6-Core Processor (€249.90 @ Caseking)
CPU Cooler: ARCTIC - Freezer 33 CPU Cooler (€30.85 @ Amazon Deutschland)
Motherboard: ASRock - Fatal1ty Z370 Gaming-ITX/ac Mini ITX LGA1151 Motherboard (€180.99 @ Amazon Deutschland)
Memory: G.Skill - Ripjaws V Series 32GB (2 x 16GB) DDR4-3200 Memory (€319.99 @ Amazon Deutschland)
Storage: Crucial - MX500 1TB M.2-2280 Solid State Drive (€190.72 @ Amazon Deutschland)
Storage: Hitachi - Travelstar 1TB 2.5" 7200RPM Internal Hard Drive (€53.48 @ Amazon Deutschland)
Case: RAIJINTEK - Metis (White) Mini ITX Tower Case (€46.71 @ Amazon Deutschland)
Power Supply: SeaSonic - FOCUS Gold 450W 80+ Gold Certified Semi-Modular ATX Power Supply (€79.00 @ Amazon Deutschland)
Total: €1151.64
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2018-07-30 07:59 CEST+0200
Few words
CPU
Put in i5-8600K to meet your 3.5Ghz and 6 core/threads requirement. i5-8400 would do as well at lower cost but it has 2.8 Ghz with 6 cores/threads. Here, it's up to you to decide which CPU to go for.
CPU cooler
For CPU cooling, put in Arctic Freezer 33 which has semi-passive fan. Meaning that when your CPU temp is below certain point, the fan doesn't turn at all, making noise output 0 dB(A). In my Skylake build (full specs with pics in my sig), i have the predecessor of Freezer 33 in use known as Freezer i32 and for me, the stock semi-passive fan didn't turn at all when my CPU temp was 52°C.
Even if you go with i5-8400, there's Intel's stock CPU cooler included with it. And while Intel's stock CPU cooler is more than enough to cool i5-8400, it's quite loud. And due to that, i suggest that you go with Freezer 33 with i5-8400 to reduce the noise.
MoBo
Since one of your requirements require Thunderbolt, i put in AsRock mini-ITX MoBo. It's the only Z370 chipset MoBo that has Thunderbolt 3 port built-in to the MoBo. While there are other Z370 chipset MoBos as well that support Thunderbolt, those require add-in card for you to use Thunderbolt. Among having Thunderbolt port on the MoBo, MoBo also has 6x USB 3.0 ports, HDMI port, built-in wi-fi and is mini-ITX in size.
RAM
Your RAM requirement of 32GB rises the PC's price considerably. Since MoBo only has 2x RAM slots and supports up to 32GB of RAM, i put in 2x 16GB 3200 Mhz RAM.
SSD
Since 1TB M.2 NVMe SSD costs a fortune, i put in 1TB M.2 ACHI SSD. Do note that while this SSD is M.2 drive, it isn't any faster than regular 2.5" SATA SSD since it uses ACHI protocol and not NVMe protocol. Still, Crucial MX500 is one of the best SSDs when it comes to the price to performance ratio and i too have the very same SSD in use with my Skylake build but mine is 2.5" from factor and not M.2 from factor.
Note: MoBo has the M.2 SSD slot at the back side.
HDD
Because you also asked for additional storage drive, i put in Hitachi 2.5" 1TB HDD at 7200 RPM. While i could also put in 3.5" HDD, i try to keep the build small and compact with minimal noise.
GPU
Didn't put dedicated GPU in since you can run your PC off from UHD 630 graphics that is built-in to the CPU. If you do need dedicated GPU then feel free to go with the one which suits your needs the most.
E.g EVGA GT 1030 with passive cooing (0 dB(A)) would suit your PC well with 1mm space to spare,
amazon.de:
https://www.amazon.de/dp/B071P2RYHG/ref=twister_B07B2PCV4P
Case
Since i'm aiming for a small footprint PC, i put in Raijntek Metis PC case. This small cube case has inverted design while having plenty of space inside for all your components, including space for up to 170mm long dedicated GPU. Since PC case comes in several different colors: black, red, silver, blue, green, gold and white, it's hard for me to pick the right color for you. So, for time being, i put in white case. Feel free to go with different colored case if you like. Oh this version is windowless but there are windowed versions in all those colors available as well,
specs:
https://www.raijintek.com/en/products_detail.php?ProductID=17
Or if you don't like this case at all, feel free to completely switch it out.
PSU
Put in good quality PSU from Seasonic. Focus 450 80+ Gold PSU is semi-modular, small in size (140mm depth) and it is powerful enough to power e.g GTX 1060 GPU if you plan to put dedicated GPU in it.
Sound card
Didn't include it since i'm not an audiophile and i don't have the know-how to suggest the best dedicated sound card to go with.
Facebook
Twitter
Instagram