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<caveat> I have done some research online recently looking for a desktop, and am by no means an expert on this subject. </caveat>
The Chipset and the bridges on the motherboard are the biggest factor on running speed.
The same hardware is attached to a Dell motherboard as an ASUS motherboard. The motherboards themselves use the same architecture, and their purported differences are usually exaggerated by their manufacturers. An IVY bridge is an IVY bridge, whatever board it's on.
What to look for in a motherboard is the connections. How many / Where are the following: USB ports, video ports, LAN port, etc.
For a given manufacturer, in general, the higher the number on the graphics card, the more powerful it is.
I've read a lot of contradictory information on how to compare graphics cards, and that little tidbit is the only really practical rule I've come up with.
Also keep in mind that more power correlates to more heat generated. As the cooling demands increase, noise generally does, too. If a quiet system is your goal, you'll likely be sacrificing graphics power to get the noise down.
You will probably want to get one with HDMI out to connect to an external monitor. Of course, your monitor needs to be HDMI, too, but it is the current standard. I don't think DVI offers as much.
I would go with the SSD if it isn't completely impractical to get your total memory up to your needs.
I'm sure portability is a concern. If you put yourself in a position where you MUST have an external hard drive, then that's more stuff to move around set up every time you use it.
Just remember to NEVER use "Disk Defragmenter" programs on an SSD. The reading and writing is what wears them out. For this reason alone, having both SSD and HDD is good, as you'll want to use the HDD for any files that get rewritten frequently.
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