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Both of these boards support the E3-1220V3 (and other Xeons) and only $130. What's wrong with those (besides that they don't support ECC)? I'm pretty sure this is what The Egg was referring to.

Depending on the state of the portable system you have, if its working, not working or just an empty case, keep in mind that it could be worth money on its own. Search for "vintage portable computer" and you'll see lots of systems going for $100-$300.

If you're thinking of doing this because you want put a lot of time into an interesting project, then go for it... but if you're trying to make it practical and inexpensive, you'll probably want to go a more traditional route. Having turned "things" into project PCs before, I can say that it will be more expensive than you think... both in time and in money. Where you'll have the most unexpected expenses will be in the little things... adapters, plates, plugs, tools, etc. And a lot of time will be spent making existing things (keyboard, buttons, switches, screen) do what you want them to do on a modern PC.

For example, an ATX system uses a momentary power switch... an AT uses a toggle switch. You flip the switch and the PC will act like you're holding the power button, so it'll shut back off. Something as simple as replacing the switch may be a pain in the butt.

If you do go ahead with this, I'd love to see it. But I wouldn't blame you for going a simpler route if you just want a small but powerful computer.

Life happened, and I can hardly believe 3 weeks went by. I apologize in advance for not being able to address the latest comments and suggestions, but I will try to make a brief update of my thoughts on this project.

I've decided that ECC RAM is too much of an expense here, in terms on money, watts, and features for what it may provide.
The ASUS H97I-PLUS looks like a winner; an on-board Displayport connection and a Mini-PCIe slot certainly would add flexibility.
I'll probably use an i7-4790S, now that it's available, though a i5-4690S is about a $100 cheaper and doesn't seem to drop that much performance (I think.)
3rd party heatsinks tend to either be too tall or too broad for reasonably quiet ones; I can simply hold off on that until a later date.
(I'm still going to go with the EVGA "superclocked" GTX 750 Ti. I haven't seen anything better without requiring additional power, which probably would be a pain to provide.)

The difficulty in selecting a power supply remains. Pretty much nothing seems to stay out of the way of the components while being orientated in any sensible direction. (Nevermind mounting it.)
I used a power supply calculator, and if I recall correctly stated a 168 watt minimum um and 207 watt recommended. I'm not quite sure those numbers; perhaps I'm mistaken about them or didn't quite understand it.

A picoPSU seems like the only thing small enough to fit, though it seems mini-box discontinues the 200W version long ago. Current ones are listed as 160W with 200W peak draw. Is that [nearly] in line with the calculated figures? I'm wondering if anyone knows of something similar or has a better suggestion for a PSU?

I noticed that TR has this PSU listed as one of their deals of the week. That's a 450W Gold Certified mini-PSU (or whatever the term is for them these days) for SFF and "slim" cases.

While an SFX format power supply unit won't work out for me, your suggestion did send me in a useful direction to search.
I can squeeze a Flex ATX PSU [a 6 inches deep model] in to where the last expansion slots would end, and then reroute the power connection using an extension with a "C13" right angle plug. Alternatively, I can slip it in the height of a single 5.25 inch drive bay and still have the second bay opening available.

Having gone back and reused power supply calculators, the highest result I was given is a 150 watt load with 200 watt PSU recommended. The closest I found in Flex ATX format was 220W, which is fine with me; it will give some ability to expand.

I'm still debating of which specific CPU I'll go with. I may not actually need more computing power than what an i5-4960S can provide, but that cut in cache to 6MB... it makes me worry about throughput for some reason.

How about a TFX PSU? It at least trades off that hissy little 40mm fan for a nice quiet 80mm one. I have the 80 Plus Bronze version for $10 less in my HTPC and it's perfectly quiet(silent).

And now it's time for me to be sheepish:
It turns out I was was wrong about the SFX PSU. One would fit perfectly behind the PCIe and above / next to the 5.25" cage, the same place I was thinking of putting a Flex ATX unit. SFX is also two inches shallower, leaving more room for the expansion card, plus can have an 80 mm intake/exhaust fan.

This one seems like the best I could find in the 200W-350W range : http://www.silverstonetek.com/product.p ... 58&area=en
The same brand as The Egg pointed out, but about $40 less, though it is only Bronze 80+ rated, rather than Gold.

Barring some last minute suggestions, I think I have all my parts picked and will order later this evening.

The parts arrived earlier in the week, so now I've started planning out the modifications to the case.
I haven't had a lot of solid free time, with only today getting the system into a temporary mATX case for stress testing and tweaking. (Any recommendation for a guide on setting up a USB stick with MEMTEST86, PRIME95, et cetera?)