Most of this makes a lot of sense to me, except the whole bit about the stroker. I think you might misunderstand something here. A 408 stroker is just a small block 360 with a 4" crank. Going to a 408 stroker won't add any weight at all, usually the stroker rotating kits end up being lighter than stock small block rotating assemblies. The pistons and rods are lighter for sure. So, the overall weight of the engine shouldn't be any different than a 340 or 360 small block. As for the 340, having built one and paid for one I wouldn't bother again, the 360's are much easier to find and a lot cheaper usually. Since nothing you do will be matching numbers I wouldn't spend the extra cash for a 340 block.
For the radiator, I think I mentioned this before, I would go straight to a 26" 3 core and run the Ford contour set up. This thread has links to both my build and goldduster318's pdf on the Contour install
Mopar Performance 360/380 running pretty hot. The thing is that black magic fan you have linked costs almost twice as much as the Contour fans, only has one speed, and only flows 3300 cfm. That would probably work, but the contour fans are OE proven parts that flow 3,500 and 5000 cfm (low and high speed) and cost less to boot.
For any electric fan set up capable of running stand alone I would say you should get a 100 amp alternator at the minimum. That's what I run, and it works well with my set up. I think the contour fans pull almost 40 amps at start up, so, even a stock 60 amp alternator would be pretty iffy.
Torsion bars I'd go with at least PST's 1.03's, if you're planning a more serious handling car Firm Feel's 1.06's or 1.12's (which is what I run) work well too. And you'll need Bilstein RCD's or Hotchkis shocks for any of those unless you hate your dental fillings and lumbar disks.
You absolutely should install subframe connectors at the minimum. Torque boxes would be very beneficial as well. And if you're looking at a handling car, some kind of foward supports (J bars or US Cartool inner fender supports) and a radiator support brace.
Doug's D453 headers will fit, so will TTI's, and I wouldn't bother spending the money on anything else. Those are both above the steering link, the other designs have tubes below the steering links and that isn't going to last on a lowered car. And they're not cheap enough to warrant buying a set to see if you smash them flat, most of them are more than half as much as the Doug's anyway, better to just do it right the first time.
I wouldn't worry about the clutch until you decide for sure on the transmission, because that will change.
Just my .02.
