Been pretty busy all week, but here's my 2 cents.
I'd buy the heads first and make sure they'll support a 347 when you want to get into it down the road. The reason being that you don't necessarily have to tear the car completely apart and can enjoy it after winter this year. Building a stroker and installing stock heads just to tear it down and install heads later seems like a waste of time to me compared to installing heads then tearing down for a complete rebuild and re-installing your "new" heads. Besides, I'm sure if you stroke it and use the stock heads, you'll be fairly disappointed in all the work you've done because you expected more. The stock heads are going to choke the extra cubes as they do with the 351's. Again, just my opinion and what I would do, take it for what it's worth.....
As for the Pro Comp heads and intake: I know nothing about the heads, but have read a few different forums about their quality being crap. I suppose if you're a machinist and don't mind setting up and re-working new heads you probably wouldn't have a problem. But for the "novice" I would recommend something a little more "name brand" if you will. AFR's are a good head from what I understand if you choose to go with them. The things to look at are spring specs (so you know if you'll have to replace them for your application), cracking (especially in the combustion area), and if the owner doesn't mind you trying this, you can fill the ports with a liquid of some sort and check the valve seal to the seat. Take some feeler gage with you and check the valve seat with it before getting water or something. A flat edge like a steel ruler to check the mating surface for flatness is a good idea. Those are the highlights of what I can think of right now and should give you a good idea if it's a good buy or not. The Pro Comp intake isn't a bad piece from what I can tell. I have the Eddy RPM Air-gap knock-off and started a thread here to give everyone an idea of what it's like. I did a little work to it and I like it a lot compared to what I had. It's currently on the second page of threads, but here is a link to it:
http://www.stangnet.com/mustang-forums/threads/pro-comp-24026-intake-manifold.883603/
And again, my personal opinion that I'm going to voice: sidepipes only belong on Shelby Cobras or mid-60s Vettes. Pretty much everything else they just look like crap. I'd keep the exhaust under the car and exit the back if you can manage it. I think you would probably be happier both with the aesthetics and not having the sound right at your left ear all the time. Again, just my opinion, take it for what it's worth as well.....
As for your shopping list, I think that includes everything except lube. Be sure you have a dial indicator, a depth micrometer would be a great idea, and if memory serves you will probably need something to measure your depth from that spans the overall distance of the housing for the depth mic. This is for setting your pinion depth. You will need either a crush sleeve or a spacer as was mentioned earlier to tighten the yoke to spec. Again, if memory serves, either the 9" or 8.8 crush sleeves work for the 8". I may be totally wrong, it's been a few years and a head injury since I've tackled mine.
But if you go by the article that I linked to before, you shouldn't have any problems getting it done.
