Dave,
The 289 and 302 block both have the same deck height and are virtually the same to answer the last question. Does your engine block have the VIN # stamped in it? I did not see you say that.
I can do some research, but to stroke to 347 on the 8.2 deck height of the 289 and 302 may require some minor notching to the bottom of the piston liner to clear the rod end caps. Not sure for the 331. This notching is minor and not a problem for longevity. The new 347 stroker kits have improved the piston pin location to allow for better oil ring sealing. The first 347 strokers had oil ring issues.
There are no longevity issues with strokers. And most kits come with premium upgrades that will last even longer. Based on equal driving habits. But with me , "mo power means mo abuse"!!!!
Your primary concern is to build a package. Your main consideration on a 289/302 is the exhaust valve size, exhaust porting, and your choice of exhaust manifolds.
You can port a stock set of 302 exhaust manifolds all you want, but they are the weak link. If you plan on these manifolds forget about stroking and forget about much of a cam or carb increase. The manifolds are too restrictive. Build a stock engine with minor upgrades such as roller rockers. Leave the heads stock.
So the next step up would be the HIPO 289 reproduction exhaust manifold. The can be ported on and will be a significant upgrade, but only so much. They will support some mild porting on the exhaust side of your head and again I would not waste any money on stroking, unless you plan exhaust flow upgrades in the future.
Next step is a shorty header.
http://www.cjponyparts.com/jba-289-...ign=shopping&gclid=CNbZ986578YCFZFgfgodUy4FdQ
These fit great and work with stock power steering hoses and no ram drop. Now you can get some exhaust flow and could build a "torque" 331 stroker. and get some value out of a roller cam and such. Larger valves and more exhaust port hogging on the heads. Roller rocker arms from Comp Cams are a smart choice for any build and cost about the same as fresh stamp steel rockers. And at this time I would opt for the screw in studs, guide plates, and short tip valve stems like the early 289 heads.
Next step is of course long tube headers.
http://www.fordpowertrain.com/347step.htm
Now you can go to the 347 stroker kit, more cam/carb and huge power. These headers tuck up very tight and do not require the PS ram to be dropped. I have them on both my cars. They will support all the HP you can develop in your basic 302 block.
The secret to 302 HP is the exhaust valve size and the exhaust porting. The intake side needs very little other than cleaning and a larger valve. Port pocketing where you remove much of the valve guide into the combustion chamber is very important. The 347 will respond well to stock "ported" iron heads with 1.6 diameter exhaust valves and either 2.02 or 1.94 valve sizes common to Chevy heads.
Do not drop below 10.0 to one compression. It will run just fine on 92 octane if properly tuned. Also remember that the 302 J Code head has the small 53 CC combustion chambers when selecting pistons.
Again, your biggest decision is the end state of you exhaust manifold or header choice. It will drive your entire build. I help people with mild to wild packages every day. You need to make the above choice and I can recommend the rest of the parts.
An (automatic overdrive (AOD) with a drop to 3.5 or 3.7 ratio rear gears is you best bang for the buck for a quick seat of the pants feel. Even with a stock motor. And way better cruising mileage. A see you have a new C4, but it needs 3.00 gears for freeway use. Huge acceleration robber!
Below is a link to an MRE book on head porting. Great info to get you up to speed. If you want to talk about this I talk way faster than I type. (360) 377-5164 9:00 a.m. to 5:00 p.m. pacific time. I have build dozens of similar motors.
Rob
http://www.mre-books.com/ford/engines/cylinder_heads.html