To start with the easy parts:
Monitor: 30" HP ZR30w or Dell's U3011 panel or whichever is the latest in the ultrasharp line for 30".
Excellent color reproduction, IPS panels, can't go wrong.
This will take about $1100-$1200 from your budget, leaving about $2800 for the rest.
There is something to be said about having a multi CPU solution, but generally you also want fast single cores, so in this budget range going with a single fast CPU is the way to go. This makes is much easier to handle the case requirement as pretty much any case will do. Memory performance does have an impact
Generally this project sounds perfect for the new intel LGA2011 CPU's and the X79 chipset. Which unfortunately is not out yet so I'll base my recommendation on a similar currently available setup. With it you can get an unlocked CPU with 6 cores and nice amount of cache for about $500 and then generally you get mobo's that support 8 DIMM slots for memory, so you can get 32GB with 8x4GB dimms. This most likely would be the perfect way to go.
CPU: i7 2600k $315
Motherboard: Asus P8Z68-V / Gen3 or similar with Gen3 support ~$200 / ASRock Z68 PROFESSIONAL GEN3 $255
Memory: 4x4GB 1.5V CAS9 1600Mhz ram ~$100 ( 4x8GB would be great, but at over 300 for 16GB it's very hard to justify the price.
CPU cooler: You probably want a good cooler for moderate overclocking on the i7 2600k.
Scythe mugen 3, Cooler Master 212 EVO $35-50.
While you might get a small improvement with either of the above.
Graphics card: NVidia GTX580 conservatively about $500
OS drive:
This really depends on how much your applications take. If they fit to 120GB with the os, then
OCZ Vertex 3 120GB for example is an excellent solution ~$200
If more is needed then you are looking at either two of the above or ~$400 or so for a 240-256GB SSD's.
Temp / work drive: Well you can get a fast SSD like the above, or a fast HDD. Or put in a raid setup.
Heavily depends on how much space is required. If 120GB will do then the SSD would be great.
If not then get a HDD Samsung Spinpoint F3 1TB x2 for example and use Raid 0 $200 for the SSD
Data HDDs:
One HDD for source. Samsung Spinpoint F3 1TB $60 - or multiples if you want a raid config
One HDD for result. Samsung Spinpoint F3 1TB $60 - or multiples if you want a raid config
Total for HDD's & SSD's about $350-$500
This will minimize cross reads/writes in the HDD's. So a single drive should only be doing one thing.
Optical: You probably need a bluray burner, so about $120 bucks for that.
Case: Silverstone Fortress FT02S $230
PSU: Seasonic X750 or one of equal quality currently $125 on sale at newegg
As for backup. Some kind of an external NAS unit with Mirrored disks would be best.
With 5400 rpm 2TB disks.
So:
CPU: i7 2600k $315
CPU cooler: Scythe Mugen 3 $50
Mobo: ASRock Z68 PROFESSIONAL GEN3 $255
Memory: Gskill 4x4GB 1.5V CAS9 1600Mhz $100
GPU: NVidia GTX580 1.5GB $500
OS Drive: OCZ Vertex 3 120GB $200
Work drive: OCZ Vertex 3 120GB $200
HDD source: 2xSamsung Spinpoint F3 1TB Raid 0 $120
HDD result: 2xSamsung Spinpoint F3 1TB Raid 0 $120
Optical: Bluray burner $120
Case: Silverstone Fortress FT02S $230
PSU: Seasonic X750 $125
Monitor: HP ZR30w $1175
Total without monitor: ~$2335
Total with monitor: ~$3510
Leaves about $500 for the backup / nas solution.
Which should be doable. Depending on the space requirements.
Total: ~4000.
The above are estimates and you can probably find many deals to get the price down.
Once the X79 comes though, I would highly recommend giving it a try instead, as it seems more suited for your situation.
While it will be slightly more expensive, it could still fit roughly into the price range.