nelsona,
There are many very good suggestions and commetn in this thread. I might add a couple of ideas based on experience with LGA1366 systems:
1. The Xeon X5690 /W3690 6-cores @ 3.47 /3.73GHz do have the highest calculation density for LGA1366. The highest Passmark average CPU mark fro the X5690 is 8936 and for the W3690 it's 9679. It's typical that CPU's made for dual use do not perform quite as well as the same specification single CPU as there are complications to synchromize the two sets of cores/threads. So, if your goal is a 6-core, a W3690 will do a bit better.
2. Also consider the CPU single thread perofmance. This will have a benefit in 3D applications- work and games included. the highest single-thread mark is using the Xeon X5687 4-core @ 3.6 /3.86 - the highest clock speed LGA1366. On Passmark, the top z400 /X5687 has a CPU score of 7363 and the single thread mark of the X5687 is 1577 as compared to X5690 with 1519 and W3690 at 1568/ again, the W3690 shows he benefit of using a single-processor configuration.
3. the RAM is triple channel so use RAM modules in sets of 3 and larger first. The best arrangment will be 6X 4GB of identical DDR3-1333.
4. There has some discussion of the disk system, but I would srecommend looking into used LSI 6GB/s RAID controller (e.g. LSI MR9460-4i) to convert the disk to something resembling SATAIII and these also allow the use os SAS drives- sometimes 125 drives! In my LGA1366 systems I use PERC H310's which are really LSI 9217's and the addition of the H310 in a Dell Precision T5500 alone changed the Passmark disk score using a Samsung 840 250GB SSD from 1940 to 2694. But, I recommend the LSI 9260.
5. Of course, significant benefit is derived from the GPU, but be aware of slightly adimishing return at the high end given the restrictions of the CPU to feed it. It's not LGA1366, but a Quadro K4200 that makes a Passmark 3D mark of 4792 in an HP z420 only produced 4076 in a Precison 390 /Xeon X3230. On that note, and based on consideration of the system value, I'm wondering if the GTX 1070 is the most sensible top end. On Passmark the highest z400 3D score is 9443 from a GTX 980 (using a W3690) and second is 8299 with a GTX 1060 (W3565). For comparison,in z420, GTX 980 is 3D rated at 9563 and second is a GTX 1060 makes 8661.
6. I'm a bit confused by the discussion on drives in this thread, but I think M.2 as a boot drive is not possible on a motherboard/.chipset /BIOS that doesn't support UEFi. A quick scan of Passmark disk listing does not show M.2 as the boot drive. The top disk score for a z400 is 5448 and the disk listed is LSI MR9460-4i as the RAID controller hides ID of the actual drives. The second fastest drisk is 4068 from a Samsung 850 Evo 500GB, and 3rd is 3918 by OCZARC100. I'm sure if M2. worked, there would be some very high scores. In a z420 / E5-1660 v2, the Samsung SM951 AHCI 256GB scores 11559.
Cheers,
BambiBoomZ